DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution - PubMed (original) (raw)

DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution

Xuhua Xia. Mol Biol Evol. 2013 Jul.

Abstract

Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).

Keywords: Gibbs sampler; bioinformatics; codon usage; dating; genomic analysis; hidden Markov model; motif discovery; phylogenetics; secondary structure.

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Figures

F<sc>ig</sc>. 1.

Fig. 1.

Gibbs sampler in action. The yeast (Saccharomyces cerevisiae) intron sequences in the top panel represent the input to the Gibbs sampler. The bottom panel represents part of the output showing the identified motif (i.e., TAATAAC, bolded) shared among the sequences. Output from DAMBE5 also includes the PWM, the significance tests associated with PWM, and the PWM scores for individual motifs as a measure of motif strength, which is correlated with slicing efficiency. The input intron sequence file (YeastAllIntron.fas) is in DAMBE installation directory in FASTA format. Modified from Xia (2012b).

F<sc>ig</sc>. 2.

Fig. 2.

Skew plots of the Bacillus subtilis genome at three different window sizes, with the skew curve colored in red having the optimal window size. The horizontal line is the global GC skew computed from the entire genome.

F<sc>ig</sc>. 3.

Fig. 3.

Hydrophobicity plot for human (NP_000530.1) and avian (Emberiza bruniceps: AFK10338) rhodopsin with seven transmembrane domains (peaks). The weak 7th peak is due to a relatively short α-helix. Output from DAMBE. A sliding window of 12 AAs is used.

F<sc>ig</sc>. 4.

Fig. 4.

Regular dating with internal node calibration (top panel) and tip dating with sampling times (specified in OTU name following “@”) for calibration, based on the LS method in DAMBE.

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