agent
e467d67723
- 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.
21 lines
513 B
Bash
21 lines
513 B
Bash
#! /bin/bash
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set -e
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SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
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if [ "$#" -ne 2 ]; then
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echo "Usage: $0 <input_fasta> <output_nexus>"
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exit 1
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fi
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in_fasta=$(readlink -f "$1")
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out_nex=$2
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# Convert fasta to nexus
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out_dir=$(dirname "$out_nex")
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mkdir -p "$out_dir"
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seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
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# append MrBayes block to nexus file
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cat "$SCRIPTS"/miscs/mbblock.txt >>"$out_nex"
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# Run MrBayes
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mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1
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