PMC:3317825 / 8846-10525
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3317825","sourcedb":"PMC","sourceid":"3317825","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3317825","text":"Phylogenetic analysis\nOf the 5014 protein families, 497 were shared by all the 29 strains and contained only a single copy from each strain (did not contain paralogs). This set of 497 single-copy core genes were identified as putative orthologous genes. The sequences were first aligned at the amino acid level using Probalign [49], then backtranslated to DNA. Alignment columns with a posterior probability \u003c 0.6 were removed, and alignments with \u003e 50% of the sites removed were discarded from the analysis. Multiple alignments with Probalign retained 491 reliably aligned genes from a set of the 497 orthologous genes. Gene trees were reconstructed using PhyML (Phylogenetic estimation using Maximum Likelihood) [50,51] with the General Time Reversible plus Gamma (GTR + G) substitution model of DNA evolution, and the Subtree Pruning-Regrafting (SPR) branch-swapping method. Each gene tree search was bootstrapped (500 pseudoreplicates) using PhyML with the Nearest-Neighbor Interchange (NNI) branch-swapping method to detect genes that support or conflict with various bipartitions. A majority rule consensus of the gene trees was constructed using the consense program of PHYLIP 3.69 [52]. All the alignments were also concatenated, and a tree search was performed using PhyML with the same settings as for the gene trees. Macrococcus caseolyticus JCSCS5402 was used as an outgroup to root the trees. We used DendroPy [53] to annotate the nodes of the estimated consensus and concatenated gene trees with the percentage of gene trees in which the node was found. Resulting phylogenetic trees were drawn using the R package APE (Analysis of Phylogenetics and Evolution) [54].","divisions":[{"label":"Title","span":{"begin":0,"end":21}}],"tracks":[{"project":"2_test","denotations":[{"id":"22272658-16954142-10678869","span":{"begin":328,"end":330},"obj":"16954142"},{"id":"22272658-20525638-10678870","span":{"begin":715,"end":717},"obj":"20525638"},{"id":"22272658-14530136-10678871","span":{"begin":718,"end":720},"obj":"14530136"},{"id":"22272658-20421198-10678872","span":{"begin":1424,"end":1426},"obj":"20421198"},{"id":"22272658-14734327-10678873","span":{"begin":1675,"end":1677},"obj":"14734327"}],"attributes":[{"subj":"22272658-16954142-10678869","pred":"source","obj":"2_test"},{"subj":"22272658-20525638-10678870","pred":"source","obj":"2_test"},{"subj":"22272658-14530136-10678871","pred":"source","obj":"2_test"},{"subj":"22272658-20421198-10678872","pred":"source","obj":"2_test"},{"subj":"22272658-14734327-10678873","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#c893ec","default":true}]}]}}