DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution

Abstract

DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently. DAMBE's new method uses all sites simultaneously for correction. DAMBE, featuring a user-friendly graphic interface, is freely available from http://dambe.bio.uottawa.ca (last accessed, April 17, 2018).

Fig. 1.

Illustration of distance imputation and estimation of the shape parameter in gamma distribution. (a) A sequence data set with S3 and S4 sharing no homologous sites to estimate distance. (b) Distance matrix with two shaded distance missing. (c) Tree reconstructed from the distance matrix in (b). (d) A case with nonunique solution for a missing distance between bonobo and chimpanzee. (e) Tree reconstructed from a multiple alignment with one site mapped to the leaves, together with one of several possible reconstruction of internal nodes. (f) Counting changes between neighboring nodes and correction for multiple hits. (g) Transitions and transversions at three sites illustrating independently estimated distance (D_IE) and simultaneously estimated distance (D_SE).