Convergence package is a software for the genome-wide detection of molecular signatures of a given phenotypic convergence.
Source code in C langage of the software are provided in directory 'src'. Directory 'data' contains a small dataset. Directory 'results' is an example of results obtained. Each directory contains a 'README.txt' file.
- file 'character.csv' contains the table giving the character "echolocation" all extant species of the dataset,
- file 'phylogeny.nwk' contains the phylogeny,
- directory 'alignments' contains a dozen of alignments of the dataset,
- file 'GO_audition.txt' contains the GO-terms related to audition,
- file 'GO_background.txt' contains the list of genes used as backgroung for the enrichment tests,
- file 'GO_description.txt' associates all GO-ident with a short description,
- file 'GO_table.csv' associates all gene idents with the GO-ident which annote it,
- file 'GO_table_audition.csv' associates all gene idents with 'audition' if they are annotated with at least a GO-terms related to audition.
the three first items are from the dataset of
Thomas, G. W. and Hahn, M. W. (2015). Determining the null model for detecting adaptive convergence from genomic data: a case study using echolocating mammals. Molecular biology and evolution, 32(5), 1232–1236