DAMBE7

DAMBE7 performs genomic and phylogenetic data analyses, including construction of large phylogenetic trees, simultaneous imputation of missing distances and phylogeny, pairwise-alignment-based phylogenetics (PhyPA) with bootstrapping and jackknifing, and estimation of rate heterogeneity via the gamma distribution shape parameter.

Key Features:

• Phylogenetic Analysis: Supports construction of large phylogenetic trees, including analyses of phage and transposon datasets, and performs simultaneous imputation of missing distances and phylogeny.
• Pairwise Alignments (PhyPA): Implements PhyPA with bootstrapping and jackknifing methods for statistical assessment of phylogenies inferred from pairwise sequence alignments.
• Rate Heterogeneity Estimation: Estimates the gamma-distribution shape parameter for rate heterogeneity over sites using a simultaneous across-sites correction for multiple hits to improve speed and accuracy.

Scientific Applications:

• Phylogenetic reconstruction: Construction and analysis of large phylogenetic trees for genomic datasets, including phage and transposon studies.
• Evolutionary rate inference: Estimation of site rate heterogeneity and the gamma-distribution shape parameter for molecular sequence data.
• Phylogenetic confidence assessment: Statistical evaluation of phylogenies derived from pairwise alignments using bootstrapping and jackknifing (PhyPA).

Methodology:

Imputation of missing distances and phylogeny simultaneously; bootstrap and jackknife resampling for PhyPA; estimation of the gamma-distribution shape parameter with simultaneous correction for multiple hits across sites.