Good day everyone,
I am to construct a phylogenetic tree with proteins but some of the homologs of the protein I am working with are truncated. How do I deal with these?
Hi Robert
I would suggest you give a try to the phylogenetic tree by using the complete and truncated sequences in a first approach. Then you can select the regions that are included in all the protein sequences (truncated and non-truncated), and do another phylogenetic tree. If you want to try some easy to use application I would recommend you
http://www.phylogeny.fr/
Best of luck.
Paco
Hi,
I also agree with Prof Francisco. For phylogenetic analysis, you need to include similar length sequences. If some of them are truncated, you can exclude those regions from the alignment files during estimation of genetic divergence. Otherwise the large truncated regions will be considered as 'deletions' and it may infer wrong relationships.
If you use a bayesian approach you are safe including up to 60% gaps in your alignment.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746219/figure/F7/
Despite other statements here, all maximum likelihood methods do not interpret a gap as a deletion by default, but rather as missing data.
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_are_gaps_and_missing_characters_treated.3F
Align all proteins, and leave in the ones with missing data. Use Maximum Likelihood methods (RAxML) to infer the tree.
Missing data cause an incorrect estimate of branch length, but should not interfere too much with topology.
Including only common areas will not improve accuracy.
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