Building Phylogenetic Tree For A 89-Sequences Msa File

Question

[layal]

I tried many online tools in order to build a phylogenetic tree from a MSA file consisting of 89 long sequences. Most of the tools gave me an error in the output stating that the file is huge or similar statements. I tried Mobyle at pasteur also, and didnt work too. any suggestions for a good reliable online tool?

[Whetting]

How long is the matrix? Must be >100K?

[layal]

Pardon me! maybe I didnt get your question, shouldn't the size of the matrix be 89x89 ? I want to get this distance matrix, and then get the tree...

[Whetting]

No problem! I was wondering how long the alignment was. Building a tree with 89 sequences should be trivial unless the sequences are really long.

Answer 1

[Hamish]

Given that the input size limits of on-line services tend to be in the 1 to 10MB region, this suggests that your sequences are very large.

In which case you will likely be better off downloading the appropriate software and performing the tree generation locally. For possible programs see:

• http://www.phylogeny.fr/version2_cgi/downloads.cgi
• http://evolution.gs.washington.edu/phylip/software.html