Tree software

[plindboe]

Sorry for a boring thread, but I'm looking for some good freeware to make phylogenetic trees. Since there are biologists and fellow biology students here I thought I'd ask.

I use Bioedit to do my sequence editing and multible alignments and that's working fine. I'm currently using a program called PHYLO_WIN to make my trees, but it has a nasty tendency to crash when there are too many sequences.

So a good, free, stable one (or just one with a 1 month free trial) is needed. Will appreciate any help.

Peter

 

[howlingwolf]

Have you tried this site? : evolution.genetics.washington.edu/phylip/software.html

It has links to a lot of software, some are free and some are not. Unfortunately it has been a long time since I had bioinformatics, but I do remember using Phylip and Mesquite to work on trees.

Good luck with your trees

Howlingwolf

 

[plindboe]

Great thanks, howlingwolf!

Peter

 

[SLP]

PHYLIP, oh my....


Actually works pretty well, but it is a DOS program and I don't think it has been updated for a decade or more.

There are a number of FREEWARE packages at the Joe Felsenstein's site, and they all have their strengths and weaknesses.

Unfortunately, I'd say your best bet in terms of flexibility, good graphical interface, printable/savable outputs, etc. is to plunk down the 85 bucks for PAUP.

 

[plindboe]

PHYLIP, oh my....


Actually works pretty well, but it is a DOS program and I don't think it has been updated for a decade or more.

Hehe, indeed I've found it kinda frustrating and primitive. But I'm sure it's alright once one gets used to it.

Unfortunately, I'd say your best bet in terms of flexibility, good graphical interface, printable/savable outputs, etc. is to plunk down the 85 bucks for PAUP.

I have wanted PAUP, but being a poor student, and not having a credit card, I've had to give up on that idea.

I don't need anything too fancy and I'd like for it to be simple to use. I just need it to do maximum parsimony, maximum likelihood, bootstrapping, and it would be nice if the trees are presented in graphic that doesn't look like DOS. Also nice if one can manipulate the trees a little afterwards, change outgroups, swap nodes and such. I'm sure with my meager demands, there should be some decent freeware programs out there.

Peter

 

[SLP]

I don't need anything too fancy and I'd like for it to be simple to use. I just need it to do maximum parsimony, maximum likelihood, bootstrapping, and it would be nice if the trees are presented in graphic that doesn't look like DOS. Also nice if one can manipulate the trees a little afterwards, change outgroups, swap nodes and such. I'm sure with my meager demands, there should be some decent freeware programs out there.

Peter

I haven't used PHYLIP since about 1997, but if I remember correctly, there are ways to 'force' certain tree topologies which in effect allows you to swap nodes and such. TREEVIEW is a nice one, but I think it only uses Macclade output files.