Computational protocol: Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacteriumtuberculosis

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Protocol publication

[…] Neighbor-joining trees were constructed using PAUP* version 4.0b10 with Jukes-Cantor distance correction (http://paup.csit.fsu.edu/). Trees were drawn using TreeView version 1.5 (http://taxonomy.zoology.gla.ac.uk/rod/treeview.html). Bootstrap analysis was performed with 1,000 replicates. Numbers of synonymous substitutions per synonymous site (Ks) and nonsynonymous substitutions per nonsynonymous site (Ka) were estimated using DNASP version 4.00, using the Nei and Gojobori method after Jukes-Cantor correction for multiple substitutions []. The program RDP version 2 [] was used to detect mosaic sequences using the Sawyer's and chi-square methods. The RDP GENECONV algorithm (which looks for regions within a sequence alignment in which sequence pairs are sufficiently similar to suspect recombination) was used for Sawyer's test, with a g-scale parameter of one and using both sequence triplets or sequence pairs scanning methods. p-Values were obtained with the KA method. The chi-square method was implemented using the MaxChi algorithm of RDP. Given an alignment, MaxChi examines sequence pairs and seeks recombination breakpoints by comparing the number of variable and nonvariable sites on both sides of the breakpoint. Split decomposition analysis was performed using SplitsTree version 4b06 []. […]

Pipeline specifications

Software tools TreeViewX, DnaSP, SplitsTree
Application Phylogenetics
Organisms Homo sapiens
Diseases Leukemia, Lymphoid, Tuberculosis