commit 1315f40, March 22, 2023
- sorted out PAML version confusion - the true PAML version 4.10.6 is now the default (compiled from github source, commit af30c37) in all scripts and in rhino/gizmo path
- added an exit with error if there's only 1 seq in the alignment
- added a test for alignments containing only 2 sequences (in which case PHYML tree building fails). I make a fake tree file (
(seq1,seq2);) and proceed with PAML. Results are pretty much meaningless for the more complex models, but I think M0 versus M0fixed might still be useful - added the ability to run the scripts on input files that are not in the current directory. Output files goes where input file are.
- now adding a first line (" numSeqs numTrees") to the tree input file for PAML, because newer codeml versions are more picky about tree format than the older versions were
- added smallDiff option to
pw_makeTreeAndRunPAML.pland to the sbatch and singularity wrappers - Fixed tsv output so that every line has the same number of columns (displays better on github)
see NEWS.md for more detail