Phase 5: selection analysis assessment¶
CodeML results assessment¶
The codeml_reader
function is designed to parse the complex CodeML directory structure and create simplified results for inexperienced users. This is achieved by incorporating in-house software CreateSummaryReport.pl
written by Dr. Thomas Walsh [Walsh, 2013] to produce the majority of the codeML results. In addition to automating CreateSummaryReport.pl
, codeml_reader
produces supplementary output files (Fig. 11) and specialized MSAs that are designed to aid in the detection of false positives (Fig. 12). If the user specifies a branch-label table (see create_branch) codeml_reader
will produce CodeML MSAs, these MSAs are characterized by the addition of i) the putative positively selected sites, and ii) the codons/amino acids that are positively selected in the respective lineage(s).
$ python vespa.py codeml_reader –input=USR_INPUT
Note
Supported file format(s): -input
: VESPA formatted codeML standard output.
Sample supplementary output file created by codeml_reader
Sample specialized MSA created by codeml_reader