diff --git a/.gitignore b/.gitignore
index b4a2e2e..cc50e9c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@
 05.reduce_redundancy/*
 05.orthology_inference/*
 06.phylogeny_reconstruction/*
+06.phylogenetic_analysis/*
 06.gene_trees/*
 10.plastid/*
 98.results/*
diff --git a/99.scripts/ticr/bucky.pl b/99.scripts/miscs/bucky.pl
similarity index 100%
rename from 99.scripts/ticr/bucky.pl
rename to 99.scripts/miscs/bucky.pl
diff --git a/99.scripts/workflow/phylogeny_reconstruction/mbblock.txt b/99.scripts/miscs/mbblock.txt
similarity index 100%
rename from 99.scripts/workflow/phylogeny_reconstruction/mbblock.txt
rename to 99.scripts/miscs/mbblock.txt
diff --git a/99.scripts/miscs/mrbayes.sh b/99.scripts/miscs/mrbayes.sh
new file mode 100644
index 0000000..318068d
--- /dev/null
+++ b/99.scripts/miscs/mrbayes.sh
@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_fasta> <output_nexus>"
+    exit 1
+fi
+
+in_fasta=$(readlink -f "$1")
+out_nex=$2
+
+# Convert fasta to nexus
+out_dir=$(dirname "$out_nex")
+mkdir -p "$out_dir"
+seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
+# append MrBayes block to nexus file
+cat "$SCRIPTS"/miscs/mbblock.txt >>"$out_nex"
+# Run MrBayes
+mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1
diff --git a/99.scripts/miscs/raxml.sh b/99.scripts/miscs/raxml.sh
new file mode 100644
index 0000000..a6a5ab0
--- /dev/null
+++ b/99.scripts/miscs/raxml.sh
@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
+    echo "Run modeltest-ng and raxml-ng on a given alignment"
+    exit 1
+fi
+
+aln=$(readlink -f "$1")
+out=$2
+threads=$3
+outgroup=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+# run modeltest-ng
+modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
+# run raxml-ng
+cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
+params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
+bash -c "$cmd $params" >/dev/null
diff --git a/99.scripts/ticr/mb.pl b/99.scripts/ticr/mb.pl
deleted file mode 100755
index 70aedbc..0000000
--- a/99.scripts/ticr/mb.pl
+++ /dev/null
@@ -1,1102 +0,0 @@
-#!/usr/bin/perl
-use strict;
-use warnings;
-use POSIX;
-use IO::Select;
-use IO::Socket;
-use Digest::MD5;
-use Getopt::Long;
-use Cwd qw(abs_path);
-use Fcntl qw(:flock);
-use File::Path qw(remove_tree);
-use Time::HiRes qw(time usleep);
-
-my $os_name = $^O;
-
-# Turn on autoflush
-$|++;
-
-# Maximum number of threads to use
-my $max_forks;
-
-# Server port
-my $port = 10002;
-
-# Stores executing machine hostnames
-my @machines;
-my %machines;
-
-# Path to text file containing computers to run on
-my $machine_file_path;
-
-# MrBayes block which will be used for each run
-my $mb_block;
-
-# Where this script is located 
-my $script_path = abs_path($0);
-
-# Directory script was called from
-my $init_dir = abs_path(".");
-
-# Where the script was called from
-my $initial_directory = $ENV{PWD};
-
-# Allow for reusing info from an old run
-my $input_is_dir = 0;
-
-# How the script was called
-my $invocation = "perl mb.pl @ARGV";
-
-# Name of output directory
-my $project_name = "mb-".int(time());
-#my $project_name = "mb-dir";
-
-# Read commandline settings
-GetOptions(
-	#"no-forks"          => \$no_forks,
-	"mb-block|m:s" => \$mb_block,
-	"machine-file:s"    => \$machine_file_path,
-	"check|c:f"         => \&check_nonconvergent,
-	"remove|r:f"        => \&remove_nonconvergent,
-    "out-dir|o=s"       => \$project_name,
-	"n-threads|T"       => \$max_forks,
-	"port=i"            => \$port,
-	"server-ip:s"       => \&client, # for internal usage only
-	"help|h"            => sub { print &help; exit(0); },
-	"usage"             => sub { print &usage; exit(0); },
-);
-
-
-# Get paths to required executables
-my $mb = check_path_for_exec("mb");
-
-my $archive = shift(@ARGV);
-
-# Some error checking
-die "You must specify an archive file.\n\n", &usage if (!defined($archive));
-die "Could not locate '$archive', perhaps you made a typo.\n" if (!-e $archive);
-die "You specified a MrBayes run archive instead of an MDL gene archive.\n" if ($archive =~ /\.mb\.tar$/);
-die "Could not locate '$machine_file_path'.\n" if (defined($machine_file_path) && !-e $machine_file_path);
-die "You must specify a file containing a valid MrBayes block which will be appended to each gene.\n\n", &usage if (!defined($mb_block));
-die "Could not locate '$mb_block', perhaps you made a typo.\n\n" if (!-e $mb_block);
-
-# Input is a previous run directory, reuse information
-$input_is_dir++ if (-d $archive);
-
-# Determine which machines we will run the analyses on
-if (defined($machine_file_path)) {
-
-	# Get list of machines
-	print "Fetching machine names listed in '$machine_file_path'...\n";
-	open(my $machine_file, '<', $machine_file_path);
-	chomp(@machines = <$machine_file>);
-	close($machine_file);
-
-	# Check that we can connect to specified machines
-	foreach my $index (0 .. $#machines) {
-		my $machine = $machines[$index];
-		print "  Testing connection to: $machine...\n";
-
-		# Attempt to ssh onto machine with a five second timeout
-		my $ssh_test = `timeout 5 ssh -v $machine exit 2>&1`;
-
-		# Look for machine's IP in test connection
-		my $machine_ip;
-		if ($ssh_test =~ /Connecting to \S+ \[(\S+)\] port \d+\./s) {
-			$machine_ip = $1;
-		}
-
-		# Could connect but passwordless login not enabled
-		if ($ssh_test =~ /Are you sure you want to continue connecting \(yes\/no\)/s) {
-			print "    Connection to $machine failed, removing from list of useable machines (passwordless login not enabled).\n";
-			splice(@machines, $index, 1);
-		}
-		# Successful connection
-		elsif (defined($machine_ip)) {
-			print "    Connection to $machine [$machine_ip] successful.\n";
-			$machines{$machine} = $machine_ip;
-		}
-		# Unsuccessful connection
-		else {
-			print "    Connection to $machine failed, removing from list of useable machines.\n";
-			splice(@machines, $index, 1);
-		}
-	}
-}
-
-print "\nScript was called as follows:\n$invocation\n";
-
-# Load MrBayes block into memory
-open(my $mb_block_file, "<", $mb_block) or die "Could not open '$mb_block': $!.\n";
-my @mb_block = <$mb_block_file>;
-close($mb_block_file);
-
-my $archive_root;
-my $archive_root_no_ext;
-if (!$input_is_dir) {
-
-	# Clean run with no prior output
-
-	# Extract name information from input file
-	($archive_root = $archive) =~ s/.*\/(.*)/$1/;
-	($archive_root_no_ext = $archive) =~ s/(.*\/)?(.*)(\.tar\.gz)|(\.tgz)/$2/;
-
-	# Initialize working directory
-	# Remove conditional eventually
-	mkdir($project_name) || die "Could not create '$project_name'$!.\n" if (!-e $project_name);
-
-	my $archive_abs_path = abs_path($archive);
-	# Remove conditional eventually
-	run_cmd("ln -s $archive_abs_path $project_name/$archive_root") if (! -e "$project_name/$archive_root");
-}
-else {
-
-	# Prior output available, set relevant variables
-
-	$project_name = $archive;
-	my @contents = glob("$project_name/*");
-
-	# Determine the archive name by looking for a symlink
-	my $found_name = 0;
-	foreach my $file (@contents) {
-		if (-l $file) {
-			$file =~ s/\Q$project_name\E\///;
-			#$archive = $file;
-			$archive = "$project_name/$file";
-			$found_name = 1;
-		}
-	}
-	die "Could not locate archive in '$project_name'.\n" if (!$found_name);
-
-	# Extract name information from input file
-	($archive_root = $archive) =~ s/.*\/(.*)/$1/;
-	($archive_root_no_ext = $archive) =~ s/(.*\/)?(.*)(\.tar\.gz)|(\.tgz)/$2/;
-}
-
-# The name of the output archive
-my $mb_archive = "$archive_root_no_ext.mb.tar";
-
-chdir($project_name);
-
-# Change how Ctrl+C is interpreted to allow for clean up
-$SIG{'INT'} = 'INT_handler';
-
-# Define and initialize directories
-my $gene_dir = "genes/";
-mkdir($gene_dir) or die "Could not create '$gene_dir': $!.\n" if (!-e $gene_dir);
-
-# Check if completed genes from a previous run exist
-my %complete_genes;
-if (-e $mb_archive) {
-	print "\nArchive containing completed MrBayes runs found for this dataset found in '$mb_archive'.\n";
-	print "Completed runs contained in this archive will be removed from the job queue.\n";
-
-	# Add gene names in tarball to list of completed genes
-	chomp(my @complete_genes = `tar tf '$mb_archive'`);
-	foreach my $gene (@complete_genes) {
-		$gene =~ s/\.tar\.gz//;
-		$complete_genes{$gene}++;
-	}
-}
-
-# Unarchive input genes 
-chomp(my @genes = `tar xvf '$init_dir/$archive' -C $gene_dir 2>&1`);
-@genes = map { s/x //; $_ } @genes if ($os_name eq "darwin");
-
-chdir($gene_dir);
-
-# Remove completed genes
-if (%complete_genes) {
-	foreach my $index (reverse(0 .. $#genes)) {
-		if (exists($complete_genes{$genes[$index]})) {
-			unlink($genes[$index]);
-			splice(@genes, $index, 1);
-		}
-	}
-}
-
-die "\nAll jobs have already completed.\n\n" if (!@genes);
-
-# Append given MrBayes block to the end of each gene
-print "\nAppending MrBayes block to each gene... ";
-foreach my $gene (@genes) {
-	open(my $gene_file, ">>", $gene) or die "Could not open '$gene': $!.\n";
-	print {$gene_file} "\n", @mb_block;
-	close($gene_file);
-}
-print "done.\n\n";
-
-# Returns the external IP address of this computer
-chomp(my $server_ip = `dig +short myip.opendns.com \@resolver1.opendns.com 2>&1`);
-if ($server_ip !~ /(?:[0-9]{1,3}\.){3}[0-9]{1,3}/) {
-	print "Could not determine external IP address, only local clients will be created.\n";
-	$server_ip = "127.0.0.1";
-}
-
-# Initialize a server
-my $sock = IO::Socket::INET->new(
-	LocalPort  => $port,
-	Blocking   => 0,
-	Reuse      => 1,
-	Listen     => SOMAXCONN,
-	Proto      => 'tcp') 
-or die "Could not create server socket: $!.\n";
-$sock->autoflush(1);
-
-print "Job server successfully created.\n";
-
-# Should probably do this earlier
-# Determine server hostname and add to machines if none were specified by the user
-chomp(my $server_hostname = `hostname`);
-if (scalar(@machines) == 0) {
-	push(@machines, $server_hostname);
-	$machines{$server_hostname} = "127.0.0.1";
-}
-elsif (scalar(@machines) == 1) {
-	# Check if the user input only the local machine in the config
-	if ($machines{$machines[0]} eq $server_ip) {
-		$machines{$machines[0]} = "127.0.0.1";
-	}
-}
-
-my @pids;
-foreach my $machine (@machines) {
-
-	# Fork and create a client on the given machine
-	my $pid = fork();	
-	if ($pid == 0) {
-		close(STDIN);
-		close(STDOUT);
-		close(STDERR);
-
-		(my $script_name = $script_path) =~ s/.*\///;
-
-		# Move required datafiles to machines, initialize clients
-		if ($machines{$machine} ne "127.0.0.1" && $machines{$machine} ne $server_ip) {
-			# Send this script to the machine
-			system("scp", "-q", $script_path, $machine.":/tmp");
-
-			# Send MrBayes executable to the machine
-			system("scp", "-q", $mb, $machine.":/tmp");
-
-			# Execute this perl script on the given machine
-			# -tt forces pseudo-terminal allocation and lets us stop remote processes
-			exec("ssh", "-tt", "$machine", "perl", "/tmp/$script_name", "--server-ip=$server_ip:$port");
-		}
-		else {
-			# Send this script to the machine
-			system("cp", $script_path, "/tmp");
-
-			# Send MrBayes executable to the machine
-			system("cp", $mb, "/tmp");
-
-			# Execute this perl script on the given machine
-			exec("perl", "/tmp/$script_name", "--server-ip=127.0.0.1:$port");
-		}
-
-		exit(0);
-	}
-	else {
-		push(@pids, $pid);
-	}
-}
-
-#chdir($gene_dir);
-
-my $select = IO::Select->new($sock);
-
-# Don't create zombies
-$SIG{CHLD} = 'IGNORE';
-
-# Stores which job is next in queue 
-my $job_number = 0;
-
-# Number of open connections to a client
-my $total_connections;
-
-# Number of complete jobs (necessary?)
-my $complete_count = 0;
-
-# Number of connections server has closed
-my $closed_connections = 0;
-
-# Minimum number of connections server should expect
-my $starting_connections = scalar(@machines);
-
-my $time = time();
-my $num_digits = get_num_digits({'NUMBER' => scalar(@genes)});
-
-# Begin the server's job distribution
-while ((!defined($total_connections) || $closed_connections != $total_connections) || $total_connections < $starting_connections) {
-	# Contains handles to clients which have sent information to the server
-	my @clients = $select->can_read(0);
-
-	# Free up CPU by sleeping for 10 ms
-	usleep(10000);
-
-	# Handle each ready client individually
-	CLIENT: foreach my $client (@clients) {
-
-		# Client requesting new connection
-		if ($client == $sock) {
-			$total_connections++;
-			$select->add($sock->accept());
-		}
-		else {
-
-			# Get client's message
-			my $response = <$client>;
-			next if (not defined($response)); # a response should never actually be undefined
-
-			# Client wants to send us a file
-			if ($response =~ /SEND_FILE: (.*)/) {
-				my $file_name = $1;
-				receive_file({'FILE_PATH' => $file_name, 'FILE_HANDLE' => $client});	
-			}
-
-			# Client has finished a job
-			if ($response =~ /DONE (.*) \|\|/) {
-				$complete_count++;				
-				printf("  Analyses complete: %".$num_digits."d/%d.\r", $complete_count, scalar(@genes));
-
-				# Perform appending of new gene to tarball in a fork as this can take some time
-				my $pid;
-				until (defined($pid)) { $pid = fork(); usleep(30000); }
-
-				if ($pid == 0) {
-
-					# Check if this is the first to complete, if so we must create the directory
-					my $completed_gene = $1;
-					if (!-e "../$mb_archive") {
-						system("touch", "$mb_archive");
-						system("tar", "cf", "../$mb_archive", $completed_gene);
-						unlink($completed_gene);
-					}
-					else {
-
-						# Obtain a file lock on archive so another process doesn't simultaneously try to add to it
-						open(my $mb_archive_file, "<", "../$mb_archive");
-						flock($mb_archive_file, LOCK_EX) || die "Could not lock '$mb_archive_file': $!.\n";
-
-						# Add completed gene
-						system("tar", "rf", "../$mb_archive", $completed_gene);
-						unlink($completed_gene);
-
-						# Release lock
-						flock($mb_archive_file, LOCK_UN) || die "Could not unlock '$mb_archive_file': $!.\n";
-						close($mb_archive_file);
-
-					}
-					exit(0);
-				}
-				else {
-					push(@pids, $pid);
-				}
-			}
-
-			# Client wants a new job
-			if ($response =~ /NEW: (.*)/) {
-				my $client_ip = $1;
-
-				# Check if jobs remain in the queue
-				if ($job_number < scalar(@genes)) {
-					printf("\n  Analyses complete: %".$num_digits."d/%d.\r", 0, scalar(@genes)) if ($job_number == 0);
-
-					my $gene = $genes[$job_number];
-
-					# Check whether the client is remote or local, send it needed files if remote
-					if ($client_ip ne $server_ip) {
-
-						# Fork to perform the file transfer and prevent stalling the server
-						my $pid;
-						until (defined($pid)) { $pid = fork(); usleep(30000); }
-
-						#my $pid = fork(); 
-						if ($pid == 0) {
-							send_file({'FILE_PATH' => $gene, 'FILE_HANDLE' => $client});	
-							unlink($gene);
-
-							print {$client} "NEW: $gene\n";
-							exit(0);
-						}
-						else {
-							push(@pids, $pid);
-						}
-					}
-					else {
-						print {$client} "CHDIR: ".abs_path("./")."\n";
-						print {$client} "NEW: $gene\n";
-					}
-					$job_number++;
-				}
-				else {
-					# Client has asked for a job, but there are none remaining
-					print {$client} "HANGUP\n";
-					$select->remove($client);
-					$client->close();
-					$closed_connections++;
-					next CLIENT;
-				}
-			}
-		}
-	}
-}
-
-# Don't think this is needed
-foreach my $pid (@pids) {
-	waitpid($pid, 0);
-}
-
-print "\n  All connections closed.\n";
-print "Total execution time: ", sec2human(time() - $time), ".\n\n";
-
-# Go back to project directory, delete empty gene dir
-chdir("..");
-&INT_handler;
-
-sub client {
-	my ($opt_name, $address) = @_;	
-
-	my ($server_ip, $port) = split(":", $address);
-
-	chdir("/tmp");
-	my $mb = "/tmp/mb";
-
-	#my $pgrp = getpgrp();
-	my $pgrp = $$;
-	setpgrp();
-
-	# Determine this host's IP
-	chomp(my $ip = `dig +short myip.opendns.com \@resolver1.opendns.com`); 
-
-	# Set IP to localhost if we don't have internet
-	if ($ip !~ /(?:[0-9]{1,3}\.){3}[0-9]{1,3}/) {
-		$ip = "127.0.0.1";
-	}
-
-	# Spawn more clients
-	my @pids;
-	# my $total_forks = get_free_cpus(); 
-	# A slightly modification in order to limit forks to 10
-	my $total_forks = 12;
-	if ($total_forks > 1) {
-		foreach my $fork (1 .. $total_forks - 1) {
-
-			my $pid = fork();
-			if ($pid == 0) {
-				last;
-			}
-			else {
-				push(@pids, $pid);
-			}
-		}
-	}
-
-	# The name of the gene we are working on
-	my $gene;
-
-	# Stores filenames of unneeded files
-	my @unlink;
-
-	# Change signal handling so killing the server kills these processes and cleans up
-	$SIG{CHLD} = 'IGNORE';
-	$SIG{HUP}  = sub { unlink($0, $mb); kill -15, $$; };
-	$SIG{TERM} = sub { unlink(glob($gene."*")) if defined($gene); exit(0)};
-
-	# Connect to the server
-	my $sock = new IO::Socket::INET(
-		PeerAddr  => $server_ip.":".$port,
-		Proto => 'tcp') 
-	or exit(0); 
-	$sock->autoflush(1);
-
-	print {$sock} "NEW: $ip\n";
-	while (chomp(my $response = <$sock>)) {
-
-		if ($response =~ /SEND_FILE: (.*)/) {
-			my $file_name = $1;
-			receive_file({'FILE_PATH' => $file_name, 'FILE_HANDLE' => $sock});	
-		}
-		elsif ($response =~ /CHDIR: (.*)/) {
-			chdir($1);
-		}
-		elsif ($response =~ /NEW: (.*)/) {
-			$gene = $1;
-
-			# Redirect STDOUT to a log file
-			open(my $std_out, ">&", *STDOUT);
-			open(STDOUT, ">", $gene.".log");
-
-			system($mb, $gene);
-
-			# Put STDOUT back to normal
-			open(STDOUT, ">&", $std_out);
-			close($std_out);
-
-			unlink($gene);
-
-			# Zip and tarball the results
-			my @results = glob($gene."*");
-			my $gene_archive_name = "$gene.tar.gz";
-			@results = grep {!/\Q$gene_archive_name\E/} @results;
-			system("tar", "czf", $gene_archive_name, @results);
-			unlink(@results);
-
-			# Send the results back to the server if this is a remote client
-			if ($server_ip ne "127.0.0.1" && $server_ip ne $ip) {
-				send_file({'FILE_PATH' => $gene_archive_name, 'FILE_HANDLE' => $sock});	
-				unlink($gene_archive_name);
-			}
-
-			# Request a new job
-			print {$sock} "DONE $gene_archive_name || NEW: $ip\n";
-		}
-		elsif ($response eq "HANGUP") {
-			last;
-		}
-	}
-
-	# Have initial client wait for all others to finish and clean up
-	if ($$ == $pgrp) {
-		foreach my $pid (@pids) {
-			waitpid($pid, 0);
-		}
-		unlink($0, $mb);
-	}
-
-	exit(0);
-}
-
-sub check_nonconvergent {
-	my ($opt_name, $threshold) = @_;	
-
-	# We have to do weird things here to get the input name
-
-	my @ARGV = split(/\s+/, $invocation);
-	shift(@ARGV); shift(@ARGV);
-
-	# Look for a directory in arguments provided
-	my $archive;
-	foreach my $arg (@ARGV) {
-		if (-d $arg) {
-			$archive = $arg;	
-		}
-	}
-
-	# Die if user didn't give us a directory
-	if (!defined($archive)) {
-		print "You must specify a directory previously generated by this script to check for nonconvergent genes.\n";
-		exit(0);
-	}
-
-	# Prior output available, set relevant variables
-
-	$project_name = $archive;
-	my @contents = glob("$project_name/*");
-
-	# Determine the archive name by looking for a symlink
-	my $found_name = 0;
-	foreach my $file (@contents) {
-		if (-l $file) {
-			$file =~ s/\Q$project_name\E\///;
-			$archive = $file;
-			$found_name = 1;
-		}
-	}
-	die "Could not locate archive in '$project_name'.\n" if (!$found_name);
-
-	chdir($project_name);
-
-	# Extract name information from input file
-	(my $archive_root = $archive) =~ s/.*\/(.*)/$1/;
-	(my $archive_root_no_ext = $archive) =~ s/(.*\/)?(.*)(\.tar\.gz)|(\.tgz)/$2/;
-
-	# Should have some completed genes in it
-	my $incomplete_archive = $archive_root_no_ext.".mb.tar";
-
-	# Check that the incomplete archive exists
-	if (!-e $incomplete_archive) {
-		print "Could not locate an archive containing completed MrBayes runs.\n";
-		exit(0);
-	}
-
-	print "\nScript was called as follows:\n$invocation\n\n";
-
-	# Create a temporary directory for our operations
-	my $check_dir = "tmp/";
-	mkdir($check_dir) if (!-e $check_dir);
-
-	$SIG{INT} = sub { remove_tree($check_dir); exit(0) };
-
-	# Open tarball in genes directory
-	chomp(my @genes = `tar xvf '$incomplete_archive' -C $check_dir 2>&1`);
-	@genes = map { s/x //; $_ } @genes if ($os_name eq "darwin");
-	@genes = sort { (local $a = $a) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					(local $b = $b) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					$a <=> $b } @genes;
-	my $longest_name_length = length($genes[$#genes]);
-	
-	print "MrBayes results available for ", scalar(@genes), " total genes:\n";
-
-	chdir($check_dir);
-
-	$SIG{INT} = sub { chdir(".."); remove_tree($check_dir); exit(0) };
-
-	# Parse log of each gene to determine final standard deviation of split frequencies
-
-	my $count = 0;
-	foreach my $gene (@genes) {
-
-		chomp(my @contents = `tar xvf '$gene' 2>&1`);
-		@contents = map { s/x //; $_ } @contents if ($os_name eq "darwin");
-
-		(my $log_file_path = $gene) =~ s/\.tar\.gz$/.log/;
-
-		# Check log file exists
-		if (!-e $log_file_path) {
-			print "Could not locate log file for '$gene'.\n";
-			exit(0);
-		}
-
-		open(my $log_file, "<", $log_file_path);
-		chomp(my @data = <$log_file>);
-		close($log_file);
-
-		my @splits = grep { /Average standard deviation of split frequencies:/ } @data;
-		my $final_split = pop(@splits);
-
-		$final_split =~ s/.*frequencies: (.*)/$1/;
-
-		#print "  $gene: $final_split\n";
-		printf("  %-${longest_name_length}s: %s\n", $gene, $final_split);
-
-		if (!defined($final_split) || $final_split > $threshold) {
-			$count++;
-		}
-		unlink(@contents);
-	}
-	printf("%d gene(s) failed to meet the threshold of %s (%.2f%%).\n", $count, $threshold, ($count / scalar(@genes) * 100));
-
-	# Clean up and exit
-	kill(2, $$);
-}
-
-sub remove_nonconvergent {
-	my ($opt_name, $threshold) = @_;	
-
-	# We have to do weird things here to get the input name
-
-	my @ARGV = split(/\s+/, $invocation);
-	shift(@ARGV); shift(@ARGV);
-
-	# Look for a directory in arguments provided
-	my $archive;
-	foreach my $arg (@ARGV) {
-		if (-d $arg) {
-			$archive = $arg;	
-		}
-	}
-
-	# Die if user didn't give us a directory
-	if (!defined($archive)) {
-		print "You must specify a directory previously generated by this script to check for nonconvergent genes.\n";
-		exit(0);
-	}
-
-	my $initial_archive = $archive;
-
-	# Prior output available, set relevant variables
-
-	$project_name = $archive;
-	my @contents = glob("$project_name/*");
-
-	# Determine the archive name by looking for a symlink
-	my $found_name = 0;
-	foreach my $file (@contents) {
-		if (-l $file) {
-			$file =~ s/\Q$project_name\E\///;
-			$archive = $file;
-			$found_name = 1;
-		}
-	}
-	die "Could not locate archive in '$project_name'.\n" if (!$found_name);
-
-	chdir($project_name);
-
-	# Extract name information from input file
-	(my $archive_root = $archive) =~ s/.*\/(.*)/$1/;
-	(my $archive_root_no_ext = $archive) =~ s/(.*\/)?(.*)(\.tar\.gz)|(\.tgz)/$2/;
-
-	# Should have some completed genes in it
-	my $incomplete_archive = $archive_root_no_ext.".mb.tar";
-
-	# Check that the incomplete archive exists
-	if (!-e $incomplete_archive) {
-		print "Could not locate an archive containing completed MrBayes runs.\n";
-		exit(0);
-	}
-
-	print "\nScript was called as follows:\n$invocation\n\n";
-
-	# Create a temporary directory for our operations
-	my $check_dir = "tmp/";
-	mkdir($check_dir) if (!-e $check_dir);
-
-	$SIG{INT} = sub { remove_tree($check_dir); exit(0) };
-
-	# Open tarball in genes directory
-	chomp(my @genes = `tar xvf '$incomplete_archive' -C $check_dir 2>&1`);
-	@genes = map { s/x //; $_ } @genes if ($os_name eq "darwin");
-	@genes = sort { (local $a = $a) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					(local $b = $b) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					$a <=> $b } @genes;
-	my $longest_name_length = length($genes[$#genes]);
-	
-	print "MrBayes results available for ", scalar(@genes), " total genes:\n";
-
-	chdir($check_dir);
-
-	$SIG{INT} = sub { chdir(".."); remove_tree($check_dir); exit(0) };
-
-	# Parse log of each gene to determine final standard deviation of split frequencies
-
-	my $count = 0;
-	foreach my $gene (@genes) {
-
-		chomp(my @contents = `tar xvf '$gene' 2>&1`);
-		@contents = map { s/x //; $_ } @contents if ($os_name eq "darwin");
-
-		(my $log_file_path = $gene) =~ s/\.tar\.gz$/.log/;
-
-		# Check log file exists
-		if (!-e $log_file_path) {
-			print "Could not locate log file for '$gene'.\n";
-			exit(0);
-		}
-
-		open(my $log_file, "<", $log_file_path);
-		chomp(my @data = <$log_file>);
-		close($log_file);
-
-		my @splits = grep { /Average standard deviation of split frequencies:/ } @data;
-		my $final_split = pop(@splits);
-
-		$final_split =~ s/.*frequencies: (.*)/$1/;
-
-		#print "  $gene: $final_split";
-		if (!defined($final_split) || $final_split > $threshold) {
-			unlink($gene);
-			#print " -- REMOVED\n";
-			printf("  %-${longest_name_length}s: %s -- REMOVED\n", $gene, $final_split);
-			$count++;
-		}
-		else {
-			printf("  %-${longest_name_length}s: %s\n", $gene, $final_split);
-			#print "\n";
-		}
-		unlink(@contents);
-	}
-	printf("%d gene(s) failed to meet the threshold of %s (%.2f%%) and have been removed.\n", $count, $threshold, ($count / scalar(@genes) * 100));
-
-	# Determine which genes met threshold and still remain
-	@genes = glob($archive_root_no_ext."*.nex.tar.gz");
-	@genes = sort { (local $a = $a) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					(local $b = $b) =~ s/.*-(\d+)-\d+\..*/$1/; 
-					$a <=> $b } @genes;
-
-	# Recreate archive with remaining genes
-	if (@genes) {
-		system("tar", "cf", $incomplete_archive, @genes);
-		unlink(@genes);
-		system("mv", $incomplete_archive, "..");
-	}
-	else {
-		# Delete the working directory if no genes meet the threshold
-		print "No genes met the threshold, removing specified directory.\n";
-
-		chdir($initial_directory);
-		$SIG{INT} = sub { remove_tree($initial_archive); exit(0) };
-	}
-
-	# Clean up and exit
-	kill(2, $$);
-}
-
-sub hashsum {
-	my $settings = shift;
-
-	my $file_path = $settings->{'FILE_PATH'};
-
-	open(my $file, "<", $file_path) or die "Couldn't open file '$file_path': $!.\n";
-	my $md5 = Digest::MD5->new;
-	my $md5sum = $md5->addfile(*$file)->hexdigest;
-	close($file);
-
-	return $md5sum;
-}
-
-sub send_file {
-	my $settings = shift;
-
-	my $file_path = $settings->{'FILE_PATH'};
-	my $file_handle = $settings->{'FILE_HANDLE'};
-
-	my $hash = hashsum({'FILE_PATH' => $file_path});
-	print {$file_handle} "SEND_FILE: $file_path\n";
-
-	open(my $file, "<", $file_path) or die "Couldn't open file '$file_path': $!.\n";
-	while (<$file>) {
-		print {$file_handle} $_;
-	}
-	close($file);
-
-	print {$file_handle} " END_FILE: $hash\n";
-
-	# Stall until we know status of file transfer
-	while (defined(my $response = <$file_handle>)) {
-		chomp($response);
-
-		last if ($response eq "TRANSFER_SUCCESS");
-		die "Unsuccessful file transfer, checksums did not match.\n" if ($response eq "TRANSFER_FAILURE");
-	}
-}
-
-sub receive_file {
-	my $settings = shift;
-
-	my $file_path = $settings->{'FILE_PATH'};
-	my $file_handle = $settings->{'FILE_HANDLE'};
-
-	my $check_hash;
-	open(my $file, ">", $file_path);
-	while (<$file_handle>) {
-		if ($_ =~ /(.*) END_FILE: (\S+)/) {
-			print {$file} $1;
-			$check_hash = $2;
-			last;
-		}
-		else {
-			print {$file} $_;
-		}
-	}
-	close($file);
-
-	# Use md5 hashsum to make sure transfer worked
-	my $hash = hashsum({'FILE_PATH' => $file_path});
-	if ($hash ne $check_hash) {
-		die "Unsuccessful file transfer, checksums do not match.\n'$hash' - '$check_hash'\n"; # hopefully this never pops up
-		print {$file_handle} "TRANSFER_FAILURE\n"
-	}
-
-	else {
-		print {$file_handle} "TRANSFER_SUCCESS\n";
-	}
-}
-
-sub INT_handler {
-
-	# Kill ssh process(es) spawn by this script
-	foreach my $pid (@pids) {
-		#kill(-1, $pid);
-		kill(15, $pid);
-	}
-
-	# Move into gene directory
-	#chdir("$initial_directory");
-	chdir("$initial_directory/$project_name");
-
-	# Try to delete directory five times, if it can't be deleted print an error message
-	# I've found this method is necessary for analyses performed on AFS drives
-	my $count = 0;
-	until (!-e $gene_dir || $count == 5) {
-		$count++;
-
-		remove_tree($gene_dir, {error => \my $err});
-		sleep(1);
-	}
-	#logger("Could not clean all files in './$gene_dir/'.") if ($count == 5);
-	print "Could not clean all files in './$gene_dir/'.\n" if ($count == 5);
-
-	exit(0);
-}
-
-sub clean_up {
-	my $settings = shift;
-
-	my $remove_dirs = $settings->{'DIRS'};
-	my $current_dir = getcwd();
-
-#	chdir($alignment_root);
-#	unlink(glob($gene_dir."$alignment_name*"));
-#	#unlink($server_check_file) if (defined($server_check_file));
-#
-#	if ($remove_dirs) {
-#		rmdir($gene_dir);
-#	}
-	chdir($current_dir);
-}
-
-sub get_num_digits {
-	my $settings = shift;
-
-	my $number = $settings->{'NUMBER'};
-
-	my $digits = 1;
-	while (floor($number / 10) != 0) {
-		$number = floor($number / 10);
-		$digits++;
-	}
-
-	return $digits;	
-}
-
-sub sec2human {
-	my $secs = shift;
-
-	# Constants
-	my $secs_in_min = 60;
-	my $secs_in_hour = 60 * 60;
-	my $secs_in_day = 24 * 60 * 60;
-
-	$secs = int($secs);
-
-	return "0 seconds" if (!$secs);
-
-	# Calculate units of time
-	my $days = int($secs / $secs_in_day);
-	my $hours = ($secs / $secs_in_hour) % 24;
-	my $mins = ($secs / $secs_in_min) % 60;
-	$secs = $secs % 60;
-
-	# Format return nicely
-	my $time;
-	if ($days) {
-		$time .= ($days != 1) ? "$days days, " : "$days day, ";
-	}
-	if ($hours) {
-		$time .= ($hours != 1) ? "$hours hours, " : "$hours hour, ";
-	}
-	if ($mins) {
-		$time .= ($mins != 1) ? "$mins minutes, " : "$mins minute, ";
-	}
-	if ($secs) {
-		$time .= ($secs != 1) ? "$secs seconds " : "$secs second ";
-	}
-	else {
-		# Remove comma
-		chop($time);
-	}
-	chop($time);
-
-	return $time;
-}
-
-sub get_free_cpus {
-
-	return $max_forks if (defined($max_forks));
-
-	my $os_name = $^O;
-
-	# Returns a two-member array containing CPU usage observed by top,
-	# top is run twice as its first output is usually inaccurate
-	my @percent_free_cpu;
-	if ($os_name eq "darwin") {
-		# Mac OS
-		chomp(@percent_free_cpu = `top -i 1 -l 2 | grep "CPU usage"`);
-	}
-	else {
-		# Linux
-		chomp(@percent_free_cpu = `top -b -n2 -d0.05 | grep "Cpu(s)"`);
-	}
-
-	my $percent_free_cpu = pop(@percent_free_cpu);
-
-	if ($os_name eq "darwin") {
-		# Mac OS
-		$percent_free_cpu =~ s/.*?(\d+\.\d+)%\s+id.*/$1/;
-	}
-	else {
-		# linux 
-		$percent_free_cpu =~ s/.*?(\d+\.\d)\s*%?ni,\s*(\d+\.\d)\s*%?id.*/$1 + $2/; # also includes %nice as free 
-		$percent_free_cpu = eval($percent_free_cpu);
-	}
-
-	my $total_cpus;
-	if ($os_name eq "darwin") {
-		# Mac OS
-		$total_cpus = `sysctl -n hw.ncpu`;
-	}
-	else {
-		# linux
-		$total_cpus = `grep --count 'cpu' /proc/stat` - 1;
-	}
-
-	my $free_cpus = ceil($total_cpus * $percent_free_cpu / 100);
-
-	if ($free_cpus == 0 || $free_cpus !~ /^\d+$/) {
-		$free_cpus = 1; # assume that at least one cpu can be used
-	}
-	
-	return $free_cpus;
-}
-
-sub run_cmd {
-	my $command = shift;
-
-	my $return = system($command);
-
-	if ($return) {
-		logger("'$command' died with error: '$return'.\n");
-		#kill(2, $parent_pid);
-		exit(0);
-	}
-}
-
-sub check_path_for_exec {
-	my $exec = shift;
-	
-	my $path = $ENV{PATH}.":."; # include current directory as well
-	my @path_dirs = split(":", $path);
-
-	my $exec_path;
-	foreach my $dir (@path_dirs) {
-		$dir .= "/" if ($dir !~ /\/$/);
-		$exec_path = abs_path($dir.$exec) if (-e $dir.$exec && -x $dir.$exec && !-d $dir.$exec);
-	}
-
-	die "Could not find the following executable: '$exec'. This script requires this program in your path.\n" if (!defined($exec_path));
-	return $exec_path;
-}
-
-sub usage {
-	return "Usage: mb.pl ([PARTITION TARBALL] [-m MRBAYES BLOCK]) || ([MRBAYES TARBALL] [-c THRESHOLD] || [-r THRESHOLD])\n";
-}
-
-sub help {
-print <<EOF; 
-@{[usage()]}
-Parallel execution of MrBayes on a large dataset
-
-  -m, --mb-block      text file containing MrBayes commands to append to each input partition (REQUIRED)
-  -c, --check         outputs how many MrBayes runs standard deviation of split frequencies have reached the specified threshold
-  -r, --remove        removes MrBayes runs with standard deviation of split frequencies below the specified threshold
-  -o, --out-dir       name of the directory to store output files in (default: "mb-" + Unix time of script invocation)
-  -T, --n-threads     the number of forks ALL hosts running analyses can use concurrently (default: current number of free CPUs)
-  --machine-file      file name containing hosts to ssh onto and perform analyses on, passwordless login MUST be enabled
-                      for each host specified in this file
-  --port              specifies the port to utilize on the server (Default: 10002)
-  -h, --help          display this help and exit
-  --usage             display proper script invocation format
-
-Examples:
-  perl mb.pl align.tgz -m bayes.txt --machine-file hosts.txt     runs MrBayes on each partition stored in align.tgz using parameters 
-                                                                 stored in bayes.txt on computers specified in hosts.txt
-  perl mb.pl align.mb.tar --check 0.02                           prints which genes in align.mb.tar have MCMC chains which reached a 
-                                                                 standard deviation of split frequencies below 0.02
-  perl mb.pl align.mb.tar --remove 0.05                          removes genes in align.mb.tar that have MCMC chains which did not reach
-                                                                 a standard deviation of split frequencies of 0.05
-
-Mail bug reports and suggestions to <noah.stenz.github\@gmail.com>
-EOF
-exit(0);
-}
diff --git a/99.scripts/workflow/orthology_inference/04.filter_ogs.sh b/99.scripts/workflow/orthology_inference/04.filter_ogs.sh
new file mode 100755
index 0000000..8b77dca
--- /dev/null
+++ b/99.scripts/workflow/orthology_inference/04.filter_ogs.sh
@@ -0,0 +1,23 @@
+#! /bin/bash
+set -e
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <out_dir> <treeshrink_dir> <min_taxon> <min_seq_length>"
+    echo "Filter orthologous groups after TreeShrink based on minimum taxon number and minimum sequence length"
+    exit 1
+fi
+
+out_dir=$(readlink -f "$1")
+treeshrink_dir=$(readlink -f "$2")
+min_taxon=$3
+min_seq_length=$4
+
+mkdir -p "$out_dir"
+for i in "$treeshrink_dir"/*/output.fasta; do
+    j=$(dirname "$i")
+    j=$(basename "$j")
+    seqlen=$(seqkit fx2tab -C ATCG "$i" | awk '{print $3}' | sort -n | head -n 1)
+    seqnum=$(grep -c ">" "$i")
+    if [[ $seqnum -eq $min_taxon && $seqlen -ge $min_seq_length ]]; then
+        cp -l "$i" "$out_dir"/"${j}.fa"
+    fi
+done
diff --git a/99.scripts/workflow/orthology_inference/09.filter_ogs.sh b/99.scripts/workflow/orthology_inference/09.filter_ogs.sh
deleted file mode 100755
index ac14150..0000000
--- a/99.scripts/workflow/orthology_inference/09.filter_ogs.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#! /usr/bin/env bash
-total_taxon=11
-min_seq_length=300
-mkdir -p final_ogs
-for i in treeshrink/* ; do
-    j=$(basename "$i")
-    seqlen=$(seqkit fx2tab -C ATCG "$i"/output.fasta | awk '{print $3}' | sort -n | head -n 1)
-    seqnum=$(grep -c ">" "$i"/output.fasta)
-    if [[ $seqnum -eq $total_taxon && $seqlen -ge $min_seq_length ]]; then
-        cp -l "$i"/output.fasta final_ogs/"${j}.fa"
-    fi
-done
diff --git a/99.scripts/workflow/phylogeny_reconstruction/01.modeltest.sh b/99.scripts/workflow/phylogeny_reconstruction/01.modeltest.sh
deleted file mode 100755
index 3ef0126..0000000
--- a/99.scripts/workflow/phylogeny_reconstruction/01.modeltest.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p modeltests
-for i in ../gene_alignment/*.fa ; do
-    j=$(basename "$i")
-    echo "modeltest-ng -p 2 -r 12345 --force -i $i -d nt -t ml -o modeltests/${j/.fa/}.modeltest" >> modeltest.cmds
-done
-xargs -t -P 4 -I cmd -a modeltest.cmds bash -c "cmd"
diff --git a/99.scripts/workflow/phylogeny_reconstruction/01.run_mrbayes.sh b/99.scripts/workflow/phylogeny_reconstruction/01.run_mrbayes.sh
new file mode 100755
index 0000000..d627a57
--- /dev/null
+++ b/99.scripts/workflow/phylogeny_reconstruction/01.run_mrbayes.sh
@@ -0,0 +1,21 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_fasta_dir> <extension> <output_dir>"
+    echo "Run MrBayes for each fasta file in the input directory"
+    exit 1
+fi
+
+input_dir=$(readlink -f "$1")
+ext=$2
+output_dir=$(readlink -f "$3")
+mkdir -p "${output_dir}"
+echo -n >mrbayes.cmds
+for f in "${input_dir}"/*."${ext}"; do
+    j=$(basename "$f" ."${ext}")
+    echo "bash $SCRIPTS/miscs/mrbayes.sh $f ${output_dir}/${j}/${j}.nex" >>mrbayes.cmds
+done
+xargs -t -P 12 -I cmd -a mrbayes.cmds bash -c "cmd"
+echo "All MrBayes analyses are done!"
diff --git a/99.scripts/workflow/phylogeny_reconstruction/02.mbsum.sh b/99.scripts/workflow/phylogeny_reconstruction/02.mbsum.sh
new file mode 100755
index 0000000..7dbe6ac
--- /dev/null
+++ b/99.scripts/workflow/phylogeny_reconstruction/02.mbsum.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+THREADS=${THREADS:-12}
+MIN_DSF=${MIN_DSF:-0.01}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <mrbayes_output_dir> <mbsum_output_dir> <num_skip>"
+    echo "Summarize MrBayes output using mbsum, skipping analyses with high DSF"
+    exit 1
+fi
+
+mb_dir=$(readlink -f "$1")
+mbsum_out_dir=$2
+num_skip=$3
+
+mkdir -p "$mbsum_out_dir"
+echo -n "" >mbsum.skip.log
+echo -n "" >mbsum.cmds
+for i in "$mb_dir"/*/mrbayes.log; do
+    og_dir=$(dirname "$i")
+    base=$(basename "$og_dir")
+    ## skip Average standard deviation of split frequencies > 0.01
+    dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "$i" 2>/dev/null)
+    if awk -v d="$dsf" -v min_dsf="$MIN_DSF" 'BEGIN{if (d >= min_dsf) exit 0; exit 1}'; then
+        echo "Skipping ${base} due to high DSF: ${dsf}" >>mbsum.skip.log
+        continue
+    else
+        echo "mbsum ${og_dir}/*.t -n $num_skip -o $mbsum_out_dir/${base}.in >> $og_dir/mbsum.log 2>&1" >>mbsum.cmds
+    fi
+done
+xargs -t -P "$THREADS" -I cmd -a mbsum.cmds bash -c "cmd"
+echo "Mbsum all done!"
diff --git a/99.scripts/workflow/phylogeny_reconstruction/02.raxml_per_gene.sh b/99.scripts/workflow/phylogeny_reconstruction/02.raxml_per_gene.sh
deleted file mode 100755
index 9736f0f..0000000
--- a/99.scripts/workflow/phylogeny_reconstruction/02.raxml_per_gene.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p raxml_ng
-echo -n > raxml_ng.cmds
-for i in modeltests/*.modeltest.out ; do
-    j=$(basename "$i")
-    cmd=$(grep "raxml-ng" "$i" | tail -n 1 | sed 's/> //')
-    echo "$cmd --all --bs-trees 1000 --outgroup Zju --redo --threads 4 --seed 12345 --prefix raxml_ng/${j/.modeltest.out/} > /dev/null" >> raxml_ng.cmds
-done
-xargs -t -P 3 -I cmd -a raxml_ng.cmds bash -c "cmd"
diff --git a/99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh b/99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh
new file mode 100755
index 0000000..1f32f66
--- /dev/null
+++ b/99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh
@@ -0,0 +1,23 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+THREADS=${THREADS:-4}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <in_dir> <out_dir> <ext>"
+    echo "Run raxml-ng on filtered orthogroup alignments"
+    exit 1
+fi
+
+in_dir=$(readlink -f "$1")
+out_dir=$2
+ext=$3
+mkdir -p "$out_dir"
+echo -n >raxml.cmds
+for i in "$in_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    out_prefix="$out_dir/${j}/${j}"
+    echo "$SCRIPTS/miscs/raxml.sh $i $out_prefix 4 Zju" >>raxml.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a raxml.cmds bash -c "cmd"
+echo "Raxml-ng all completed."
diff --git a/99.scripts/workflow/phylogeny_reconstruction/07.mbsum.sh b/99.scripts/workflow/phylogeny_reconstruction/07.mbsum.sh
deleted file mode 100755
index 7d765fb..0000000
--- a/99.scripts/workflow/phylogeny_reconstruction/07.mbsum.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env bash
-
-mkdir -p ../mbsum_out
-echo -n "" > ../mbsum.log
-for i in *.nex.tar.gz; do
-    base=$(basename "$i" .nex.tar.gz)
-    echo "Processing ${base}" >> ../mbsum.log
-    mkdir -p "${base}"
-    tar -xzf "$i" -C "${base}"
-    ## skip Average standard deviation of split frequencies > 0.01
-    dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "${base}"/*.nex.log 2>/dev/null)
-    if awk -v d="$dsf" 'BEGIN{if (d >= 0.01) exit 0; exit 1}'; then
-        echo "Skipping ${base} due to high DSF: ${dsf}" >> ../mbsum.log
-        continue
-    else
-        mbsum "${base}"/*.t -n 1000 -o ../mbsum_out/"${base}".in >> ../mbsum.log 2>&1
-    fi
-    rm -rf "${base}"
-    echo "Completed ${base}" >> ../mbsum.log
-done
-echo "All done!"
diff --git a/pixi.lock b/pixi.lock
index 1aa5e90..5e58bac 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -1,5 +1,78 @@
 version: 6
 environments:
+  beast:
+    channels:
+    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
+    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    packages:
+      linux-64:
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/alsa-lib-1.2.15.1-hb03c661_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/beagle-lib-4.0.1-h9948957_3.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/beast-10.5.0-hdfd78af_0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/fonts-conda-forge-1-hc364b38_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/harfbuzz-12.2.0-h15599e2_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/icu-75.1-he02047a_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libcups-2.3.3-hb8b1518_5.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libdeflate-1.25-h17f619e_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libfreetype6-2.14.1-h73754d4_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libglib-2.86.3-h6548e54_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libjpeg-turbo-3.1.2-hb03c661_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libpng-1.6.53-h421ea60_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_16.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libuuid-2.41.2-h5347b49_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libwebp-base-1.6.0-hd42ef1d_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/openjdk-25.0.1-h5755bd7_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/openssl-3.6.0-h26f9b46_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pixman-0.46.4-h54a6638_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libice-1.1.2-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libx11-1.8.12-h4f16b4b_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxau-1.0.12-hb03c661_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb03c661_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxext-1.3.6-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxfixes-6.0.2-hb03c661_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxi-1.8.2-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxrandr-1.5.4-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxrender-0.9.12-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxt-1.3.1-hb9d3cd8_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
   default:
     channels:
     - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
@@ -22,8 +95,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/augustus-3.5.0-pl5321h57ba348_8.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/bamtools-2.5.3-he132191_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/bbmap-39.37-he5f24ec_0.conda
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/beagle-lib-4.0.1-h9948957_3.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/beast-10.5.0-hdfd78af_0.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/beagle-lib-3.1.2-h503566f_5.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/binutils_impl_linux-64-2.45-h9d8b0ac_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/bioconductor-annotate-1.84.0-r44hdfd78af_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/bioconductor-annotationdbi-1.68.0-r44hdfd78af_0.tar.bz2
@@ -239,6 +311,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libldl-3.3.2-hf02c80a_7100101.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libllvm20-20.1.8-hecd9e04_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libllvm21-21.1.0-hecd9e04_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libltdl-2.4.3a-h5888daf_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libmamba-2.3.2-hae34dd5_2.conda
@@ -272,6 +345,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsuitesparseconfig-7.10.1-h901830b_7100101.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsystemd0-257.10-hd0affe5_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtool-2.5.4-h5888daf_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtorch-2.6.0-cpu_generic_haed06de_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libumfpack-6.3.5-h873dde6_7100101.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2
@@ -312,6 +386,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mpg123-1.32.9-hc50e24c_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/mpmath-1.3.0-pyhd8ed1ab_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/mrbayes-3.2.7-hd0d793b_7.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/muscle-3.8.1551-h9948957_9.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda
@@ -337,7 +412,6 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/ossuuid-1.6.2-h5888daf_1001.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/p7zip-16.02-h9c3ff4c_1001.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/pal2nal-14.1-pl5321hdfd78af_3.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/paml-4.10.9-h7b50bb2_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pandas-2.3.3-py311hed34c8f_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pandoc-3.8.2.1-ha770c72_0.conda
@@ -370,7 +444,6 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-which-1.24-pl5321hd8ed1ab_0.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/perl-inc-latest-0.500-pl5321ha770c72_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/perl-io-compress-2.213-pl5321h503566f_0.conda
@@ -728,88 +801,6 @@ environments:
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       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
-  mrbayes:
-    channels:
-    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
-    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
-    - url: https://conda.anaconda.org/conda-forge/
-    - url: https://conda.anaconda.org/bioconda/
-    packages:
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-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
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   sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
@@ -846,6 +837,16 @@ packages:
   license_family: GPL
   size: 566531
   timestamp: 1744668655747
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/alsa-lib-1.2.15.1-hb03c661_0.conda
+  sha256: 224f1a55a9ba7e877bce980f14fc3e3c0f0fb6d3cbf3c5f1a8f5dd8391ce8bba
+  md5: bba37fb066adb90e1d876dff0fd5d09d
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+  - libgcc >=14
+  license: LGPL-2.1-or-later
+  license_family: GPL
+  size: 585491
+  timestamp: 1766155792553
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
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@@ -3515,6 +3516,18 @@ packages:
   license_family: MIT
   size: 74811
   timestamp: 1752719572741
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda
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+  depends:
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+  - libgcc >=14
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+  license: MIT
+  license_family: MIT
+  size: 76643
+  timestamp: 1763549731408
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda
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@@ -3572,6 +3585,19 @@ packages:
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   size: 822552
   timestamp: 1759968052178
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda
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+  depends:
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+  - _openmp_mutex >=4.5
+  constrains:
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+  - libgomp 15.2.0 he0feb66_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 1042798
+  timestamp: 1765256792743
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/libgcc-devel_linux-64-15.2.0-h73f6952_107.conda
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   timestamp: 1759967882886
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda
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+  license: GPL-3.0-only WITH GCC-exception-3.1
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@@ -3686,6 +3721,21 @@ packages:
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   timestamp: 1762787455198
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libglib-2.86.3-h6548e54_0.conda
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+  md5: 034bea55a4feef51c98e8449938e9cee
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+  - libiconv >=1.18,<2.0a0
+  - libzlib >=1.3.1,<2.0a0
+  - pcre2 >=10.47,<10.48.0a0
+  constrains:
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+  license: LGPL-2.1-or-later
+  size: 3946542
+  timestamp: 1765221858705
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda
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   timestamp: 1759967942498
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda
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+  license_family: GPL
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 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libheif-1.19.7-gpl_hc18d805_100.conda
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   license: zlib-acknowledgement
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   timestamp: 1753879899951
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libpng-1.6.53-h421ea60_0.conda
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+  - libzlib >=1.3.1,<2.0a0
+  license: zlib-acknowledgement
+  size: 317748
+  timestamp: 1764981060755
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@@ -4236,6 +4305,18 @@ packages:
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+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda
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+  - libgcc 15.2.0 he0feb66_16
+  constrains:
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+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 5856456
+  timestamp: 1765256838573
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/libstdcxx-devel_linux-64-15.2.0-h73f6952_107.conda
   sha256: ae5f609b3df4f4c3de81379958898cae2d9fc5d633518747c01d148605525146
   md5: a888a479d58f814ee9355524cc94edf3
@@ -4254,6 +4335,15 @@ packages:
   license_family: GPL
   size: 29343
   timestamp: 1759968157195
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_16.conda
+  sha256: 81f2f246c7533b41c5e0c274172d607829019621c4a0823b5c0b4a8c7028ee84
+  md5: 1b3152694d236cf233b76b8c56bf0eae
+  depends:
+  - libstdcxx 15.2.0 h934c35e_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 27300
+  timestamp: 1765256885128
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsuitesparseconfig-7.10.1-h901830b_7100101.conda
   sha256: d8f32a0b0ee17fbace7af4bd34ad554cc855b9c18e0aeccf8395e1478c161f37
   md5: 57ae1dd979da7aa88a9b38bfa2e1d6b2
@@ -4374,6 +4464,16 @@ packages:
   license_family: MIT
   size: 85741
   timestamp: 1757742873826
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libuuid-2.41.2-h5347b49_1.conda
+  sha256: 030447cf827c471abd37092ab9714fde82b8222106f22fde94bc7a64e2704c40
+  md5: 41f5c09a211985c3ce642d60721e7c3e
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 40235
+  timestamp: 1764790744114
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda
   sha256: e5ec6d2ad7eef538ddcb9ea62ad4346fde70a4736342c4ad87bd713641eb9808
   md5: 80c07c68d2f6870250959dcc95b209d1
@@ -5116,16 +5216,6 @@ packages:
   license_family: APACHE
   size: 62477
   timestamp: 1745345660407
-- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/pal2nal-14.1-pl5321hdfd78af_3.tar.bz2
-  sha256: aff933ffefe2ecbc31b6e38bbbb2a19b5b34c2942b3d2078d7f5848432d494f6
-  md5: 2afdf27b9f28038bfb670e2059deca04
-  depends:
-  - perl >=5.32.1,<6.0a0 *_perl5
-  - perl-getopt-long
-  license: GPLv2.0
-  license_family: GPL
-  size: 22693
-  timestamp: 1642293349880
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/paml-4.10.9-h7b50bb2_1.conda
   sha256: 81c5237b07796984d7915d29a768068a1e5e6c02b4ae25f27836b0babe84e5aa
   md5: ef02b401c5daaf104b3d1091f8ec37f5
@@ -5260,6 +5350,18 @@ packages:
   license_family: BSD
   size: 1209177
   timestamp: 1756742976157
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
+  sha256: 5e6f7d161356fefd981948bea5139c5aa0436767751a6930cb1ca801ebb113ff
+  md5: 7a3bff861a6583f1889021facefc08b1
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - bzip2 >=1.0.8,<2.0a0
+  - libgcc >=14
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 1222481
+  timestamp: 1763655398280
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda
   build_number: 7
   sha256: 9ec32b6936b0e37bcb0ed34f22ec3116e75b3c0964f9f50ecea5f58734ed6ce9
@@ -5515,14 +5617,6 @@ packages:
   license_family: OTHER
   size: 17329
   timestamp: 1636695979827
-- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2
-  sha256: 94c17b270316f9b38cf1afa0b1724cdb6bd8349207568dccc1156b9014708c7d
-  md5: 10469a3defbd6dbab17d3d10dd6fd828
-  depends:
-  - perl >=5.32.1,<6.0a0 *_perl5
-  license: unknown
-  size: 33785
-  timestamp: 1718113256479
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2
   sha256: f40d5302de8c81282b5216edd8c65aecc551ef725db3351c208bff9b077e66a2
   md5: 66e17c342d13c39a12c1059f13f9b72c
@@ -10260,6 +10354,16 @@ packages:
   license: BSD-3-Clause
   size: 466893
   timestamp: 1762512695614
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 601375
+  timestamp: 1764777111296
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
   sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
   md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
diff --git a/pixi.toml b/pixi.toml
index 613d196..265221e 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -15,8 +15,6 @@ index-url = "https://mirrors.bfsu.edu.cn/pypi/web/simple"
 
 [tasks]
 
-[dependencies]
-
 [feature.base.dependencies]
 sra-tools = "*"
 fastp = "*"
@@ -31,20 +29,17 @@ pip = ">=25.2,<26"
 seqkit = ">=2.10.1,<3"
 r-rstan = ">=2.32.7,<3"
 biopython = ">=1.85,<2"
-pal2nal = ">=14.1,<15"
 trimal = ">=1.5.0,<2"
 treeshrink = ">=1.3.9,<2"
 r-ape = ">=5.8_1,<6"
 raxml-ng = ">=1.2.2,<2"
 modeltest-ng = ">=0.1.7,<0.2"
-beast = ">=10.5.0,<11"
 aster = ">=1.23,<2"
 julia = "1.12.*"
 conda = ">=25.9.1,<26"
 r-phangorn = ">=2.12.1,<3"
 r-languageserver = ">=0.3.16,<0.4"
 seqmagick = ">=0.8.6,<0.9"
-beagle-lib = "4.*"
 maven = ">=3.9.11,<4"
 matplotlib = ">=3.10.8,<4"
 ete3 = ">=3.1.3,<4"
@@ -54,12 +49,13 @@ macse = ">=2.7,<3"
 td2 = ">=1.0.6,<2"
 mmseqs2 = ">=18.8cc5c,<19"
 paml = ">=4.10.9,<5"
+beagle-lib = "==3.1.2"
+mrbayes = ">=3.2.7,<4"
 
-[feature.mrbayes.dependencies]
-beagle-lib = ">=3.1.2,<4"
-mrbayes = ">=3.2.7"
+[feature.beast.dependencies]
+beagle-lib = ">=4.0.1,<5"
+beast = ">=10.5.0,<11"
 
 [environments]
 default = ["base"]
-mrbayes = ["mrbayes"]
-
+beast = ["beast"]