Build Gene Tree for a set of homologously related genes in a FeatureSet
This App allows the user to build a phylogenetic tree of related protein encoding genes using the amino acid sequences.
Running this App is the functional equivalent to running each of the Apps in the Build a Gene Tree Tutorial Narrative, but is invoked as a single App. It includes the same parameters as would be given to each of the steps separately, starting with MUSCLE to build the initial Multiple Sequence Alignment (MSA), then Gblocks to trim the MSA to the less variable regions, and finally FastTree-2 to build the phylogenetic inference from the distances between the sequences in the MSA.
MUSCLE performs a Multiple Sequence Alignment (MSA) of homologously related sequences.
Gblocks trims Multiple Sequence Alignments (MSAs) to capture the conserved blocks that may be more reliable regions from which to compare evolutionary rates, such as for tree building. Gblocks 0.91b from http://molevol.cmima.csic.es/castresana/Gblocks.html
FastTree-2 builds a Phylogenetic Tree reconstruction from a Multiple Sequence Alignment (MSA) of protein sequences. Tree display uses ETE3 (v3.0.0b35). FastTree2.1.9 from http://www.microbesonline.org/fasttree/
Team members who developed & deployed algorithm in KBase:Dylan Chivian.
Related Publications
- Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792 1797. doi:10.1093/nar/gkh340 , https://academic.oup.com/nar/article/32/5/1792/2380623
- MUSCLE 3.8.425 from , http://www.drive5.com/muscle/
- Castresana J. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. Mol Biol Evol. 2000;17: 540 552. doi:10.1093/oxfordjournals.molbev.a026334 , https://academic.oup.com/mbe/article/17/4/540/1127654
- Talavera G, Castresana J, Kjer K, Page R, Sullivan J. Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments. Syst Biol. 2007;56: 564 577. doi:10.1080/10635150701472164 , https://academic.oup.com/sysbio/article/56/4/564/1682121
- Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016;33: 1635 1638. doi:10.1093/molbev/msw046 , https://www.ncbi.nlm.nih.gov/pubmed/26921390
- ETE3 source: , http://etetoolkit.org
- Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26: 1641 1650. doi:10.1093/molbev/msp077 , https://www.ncbi.nlm.nih.gov/pubmed/19377059
- Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLOS ONE. 2010;5: e9490. doi:10.1371/journal.pone.0009490 , https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009490
App Specification:
https://github.com/kbaseapps/kb_phylogenomics/tree/7a7953cfae374968499ac49d7716ce9bc99b2ca0/ui/narrative/methods/build_gene_treeModule Commit: 7a7953cfae374968499ac49d7716ce9bc99b2ca0