RAxML input file format

[jings]

I can not get that Phylip format CIPRES webpage showed.

I used all kinds of software, also, I used Readseq in CIPRES, I just get a normal Phylip format file. 

So, I wonder if somebody can give me an instruction about how can I get the correct Phylip format file? What software I should use?

[Nate]

I'm having the same problem. I've tried converting sequences from Nexus here:

http://www.ebi.ac.uk/cgi-bin/readseq.cgi

and

http://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html

and using MEGA 5 to output directly.

Nothing works. This is why I really hate phylogenetics software. Every new piece of software that comes out has some random frigging quirk that takes hours to solve. It's the same old song and dance every time. I wish some of these programmer geniuses would spend a little more time on the frontend of this stuff.  rant over

[Jing Sun]

Hi,

I Just don't put the outgroup species  when I used the CIPRES RAxML, then it works.

hope this helps you.

Jing

2012/9/9 Nate <twa...@gmail.com>

--
Jing Sun

Phone: 319-855-3373

[Ingo Michalak]

Nate,

compatibility issues are definitely not restricted to phylogenetics software and you will have to find your ways to convert your data properly for your needs in (I guess) what ever field you are. Maybe I can help telling how I normally handle file conversion for the use in RAxML:

As many programs understand under "Phylip format" a slight different thing than RAxML does (namely a much more restricted format, in which, e.g., all taxon names are restricted to 10 chars), I usually export my data from wherever I come to Nexus (sequential), and then open the produced file in a text editor (e.g. textmate or textwrangler on OSX, notepad++ on Windows) to then 

*get rid of all the meta information in the Nexus file (as "Data" or other blocks), just leave the taxon names and matrix (without the word 'matrix') and in the first line the number of taxa and number of characters, separated by a space.

*use the search and replace function (maybe in combination with regular expressions) to

*get rid of all the following characters, as they are not allowed in Phylip: , ’ ) ( : ; ] [ 

*get rid of all spaces in the taxon names

Following those four easy steps should provide you with a fully RAxML-compatible phylip file.

Best

Ingo

[Jing Sun]

Hi,

Great!

I agree.

Thank U!

Jing

2012/9/10 Ingo Michalak <boro...@gmail.com>

[Alexis]

However posts messages as the one below in here will be immediately removed from the forum.

Alexis

Am Montag, 10. September 2012 05:39:08 UTC+2 schrieb Nate: