Add scripts for phylogenetic analysis using MrBayes and RAxML

- Created `mbblock.txt` for MrBayes configuration.
- Implemented `mrbayes.sh` to convert FASTA to Nexus and run MrBayes.
- Developed `raxml.sh` to run modeltest-ng and raxml-ng on alignments.
- Added `04.filter_ogs.sh` to filter orthologous groups based on taxon count and sequence length.
- Implemented `01.run_mrbayes.sh` to execute MrBayes for multiple FASTA files.
- Created `02.mbsum.sh` to summarize MrBayes output while skipping high DSF analyses.
- Developed `03.run_raxml.sh` to run raxml-ng on filtered alignments.

99.scripts/miscs/mbblock.txt

@@ -0,0 +1,12 @@
+begin mrbayes;
+set nowarnings=yes;
+set usebeagle=yes;
+set autoclose=yes;
+set seed=12345;
+set swapseed=12345;
+lset nst=6 rates=gamma;
+mcmcp ngen=2000000 burninfrac=.25 samplefreq=1000 printfreq=10000 checkpoint=no
+diagnfreq=10000 nruns=3 nchains=3 temp=0.40 swapfreq=10 stoprule=no;
+mcmc;
+sumt;
+end;