DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution

Abstract

DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data with a user-friendly Windows 95/98/2000/NT interface. DAMBE is free and can be downloaded from http://web.hku.hk/~xxia/software/software.htm. The current version is 4.0.36.

Amphibians crossing the Bering Land Bridge: Evidence from holarctic treefrogs (Hyla, Hylidae, Anura)

“…To examine substitution saturation, the number of transitions and transversions versus TN93 distance were plotted for all genes and the three codon positions of protein-coding genes in DAMBE (Xia and Xie, 2001). Additionally, we conducted the incongruence length difference (ILD) test (Farris et al, 1994) with 1000 replicates and 10 random sequence additions as implemented in PAUP 4.10b (Swofford, 2003).…”

Phylogenetic relationships and evolution of pulmonate gastropods (Mollusca): New insights from increased taxon sampling

“…Regions with ambiguous positions that could not be aligned were difficult to identify manually and were removed using Gblocks (Castresana, 2000), with the 37, 95, 102-104, 165-176, 182, 206, 211-262, 268-84, 298, 325-328, 366, 382, 397, 421, 530, 551, 741-1008, 1022-1023, 1045, 1121-1124, 1128, 1170-1171, 1189-1191, 1293, 1395, 1719-1923, 2254-2264, 2272-2273, 2284-2286. Substitution saturation was measured using Xia's test (Xia et al, 2003;Xia and Lemey, 2009) implemented in DAMBE (Xia and Xie, 2001). No saturation was detected in the 16S alignment (321 sites) from which gaps and ambiguous regions had been removed (Iss significantly < Iss.c).…”

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

“…Gaps were considered as missing data rather than fifth characters, to prevent those longer than one or two bases from being taken as representing multiple events (Swofford, 1993). Pairwise distances based on the F84 model (Felsenstein, 1993) were calculated with the DAMBE program (Xia and Xie, 2001). Stationarity of nucleotide composition across taxa were examined using chi-square (v 2 ) tests implemented in PAUP* 4.0b10 (Swofford, 2002).…”