frezien, on May 18 2009, 04:08 AM, said:
Hello anyone! I'm looking for some phylogeny reconstruction software which allows to use more sequences per one taxon. I have 16 species of plants from genos Eleocharis. From every single species I have from 2 to 14 partial sequences of reverse transcriptases of copia retrotransposons. Now I would like to use these sequences to reconstruct phylogenetic relationships between those 16 species. To date I was only able to produce distance matrix (using grouping of sequences in MEGA 4.0) from which I can construct the tree, but I'm unable to use bootstraping. I hope you understand what I'm looking for. Thanks for any answer or advice.
The easiest way to do this is with sequence concatenation, e.g.
Seq 1: ABCDEF
Seq 2: GHIJKLM
Concat 1: ABCDEFGHIJKLM
You then need, ideally, to use software that allows partitioning of data e.g. RAxML or MrBayes, to assign different model of evolution to each part of the concatenated sequence and then run it as a normal phylogeny...