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.
12 lines
298 B
Plaintext
12 lines
298 B
Plaintext
begin mrbayes;
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set nowarnings=yes;
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set usebeagle=yes;
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set autoclose=yes;
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set seed=12345;
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set swapseed=12345;
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lset nst=6 rates=gamma;
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mcmcp ngen=2000000 burninfrac=.25 samplefreq=1000 printfreq=10000 checkpoint=no
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diagnfreq=10000 nruns=3 nchains=3 temp=0.40 swapfreq=10 stoprule=no;
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mcmc;
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sumt;
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end; |