Phylogeny and motifs search questions

Question

[dinber19]

Hi all,

I was wondering if you can help me with the following questions:

1. I have a protein data, that I ran in MEME and found an interesting motif. However, TOMTOM is only suitable for DNA or RNA sequences. I want to find annotations and information on this motif, using similar program to TOMTOM but one that is compatible for proteins, Do you know any I can use?

2. I need a program that can create a phylogeny tree that has no limitation on organism name length or character type (for example + can be used), and can run up to 300000 of total sequence length (amino acids if it makes a difference).

I tried Bosque 2.0 but it keeps crashing.

Thank you,

Dina

Answer 1

[jhc]

For

1. you could try SMART,
2. there are plenty of options. The choice would depend on what type of inference you want to use. Raxml, Phyml, FastTree, PhyloBayes, IQTree... all those programs will run fine, although some may take very long to compute large trees. If you need to run a complete workflow (i.e. alignment+tree inference), ete-build may help. Check also MEGA, a popular all-in-one software.