IUBio

Reading and writing NEXUS: C source code wanted

francis at CMMT.UBC.CA francis at CMMT.UBC.CA
Wed May 5 15:39:39 EST 1999


> From: Jonathan Epstein <Jonathan_Epstein at nih.gov>
> Subject: Re: Reading and writing NEXUS: C source code wanted
> Date: Wed, 05 May 1999 13:26:40 -0400


> The file desktop/salfiles.c in the NCBI toolkit seems to meet many of
> your needs, although I don't know how comprehensively it parses Nexus.

(Hi Jonathan :-)

Sequin (in the NCBI toolkit) reads Nexus files, so I'm pretty sure 
the URL Jonathan provided below will have what you need.

cheers,

f.

--
| B.F. Francis Ouellette                     tel: (604) 875-3815  | 
| Director, Bioinformatics Core Facility     fax: (604) 875-3840  | 
| Centre for Molecular Medicine and Therapeutics, UBC, Canada     |
| francis at cmmt.ubc.ca                     http://www.cmmt.ubc.ca  |



> You can get the toolkit from
>   ftp://ncbi.nlm.nih.gov/toolbox/
> 
> Good luck,
> 
> - Jonathan
> 
> Daniel Barker wrote:
> > 
> > I am looking for a library to read and write NEXUS files (Maddison et al.
> > 1997). I would like this to be (1) written in ANSI C, (2) portable, (3)
> > thoroughly tested and stable, (4) available as source code, (5) free and
> > (6) either released from copyright or distributed under a licence which
> > allows free re-distribution.
> > 
> > So far, I have come across the following, which could be helpful in
> > implementing such a C library but do not constitute one themselves:
> > 
> > Visual Basic source code by N. Cathness at
> > http://research.amnh.org/~neil/nexus.html
> > 
> > PASCAL-like pseudocode by D. R. Maddison, D. L. Swofford and
> > W. P. Maddison at http://phylogeny.arizona.edu/nexus/reading.html
> > 
> > I would be grateful for advice on further resources, or any other
> > information. Thank you.
> > 
> > REFERENCE
> > 
> > Maddison, D. R., Swofford, D. L. & Maddison, W.P. 1997. "NEXUS: an
> > extensible file format for systematic information." Systematic
> > Biology 46(4): 590-621
> > 
> > Daniel Barker.
> 





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