Adding a new gene to a precomputed gene tree ?
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5.7 years ago

Suppose I have a new gene assigned to a gene family. I also have a precomputed gene tree for this family. Is there a method to add the gene in the tree without having to compute a new MSA and avoiding to perform de novo tree reconstruction. I know that some multiple sequence aligners can add a new sequence to a precomputed MSA (ie MAFFT...). But what about tree reconstruction ?

phylogeny alignment gene tree • 2.1k views
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Without rebuilding the tree from the alignment, how would you know where to insert the new gene ? Also how you would add the new gene to an existing tree would depend on how the tree was constructed i.e. maximum likelihood vs parsimony.

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treebest can constrain the tree to the one provided with the -c option

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Thanks. Indeed TreeBeST is taking a species tree and can infer the orthologs and within-species paralogs.

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You are right. But what I expect is to obtain a tree using the computed tree as guide. But perhaps this has no sense!

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5.7 years ago
lh3 32k

Treebest as Jean-Karim (hello!) said. Two possible ways. First, you can use neighbor-joining:  treebest nj -c known.nh aln.mfa  Treebest will not change the topology of known.nh even if the alignment strongly suggest a different one. Second, you can use an old Phyml:  treebest phyml -C known.nh aln.mfa  With the phyml command, you may also consider to change option -p as it may change the known tree topology when the alignment is strongly against it.

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5.7 years ago
Steven Lakin ★ 1.7k

If you have the distance matrix from which the tree was built, you simply have to do a pairwise alignment between your new sequence and each of the others; that new vector of pairwise distances will become the new column in your distance matrix, then you can rebuild the tree. If you don't have the distance matrix, then you'll have to redo the MSA.