head	1.3;
access;
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	RELEASE_8_3_0:1.2
	RELEASE_9_0_0:1.2
	RELEASE_7_4_0:1.1
	RELEASE_8_2_0:1.1
	RELEASE_6_EOL:1.1
	RELEASE_8_1_0:1.1
	RELEASE_7_3_0:1.1
	RELEASE_8_0_0:1.1;
locks; strict;
comment	@# @;


1.3
date	2013.02.04.13.32.33;	author svnexp;	state Exp;
branches;
next	1.2;

1.2
date	2011.03.19.12.29.36;	author miwi;	state Exp;
branches;
next	1.1;

1.1
date	2009.07.21.01.10.13;	author amdmi3;	state Exp;
branches;
next	;


desc
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1.3
log
@## SVN ## Exported commit - http://svnweb.freebsd.org/changeset/base/311601
## SVN ## CVS IS DEPRECATED: http://wiki.freebsd.org/CvsIsDeprecated
@
text
@SHA256 (phyml/phyml-20120412.tar.gz) = a43e51534a1ae2d1ee4c94ced3a1855813ff4872a6c9c2b83b369ddb71198417
SIZE (phyml/phyml-20120412.tar.gz) = 4089133
SHA256 (phyml/20121109.patch) = 3aa8bebd0ff78a553795ddda512ef1c7542d1e3c90c1da61c7125c304f6caa2c
SIZE (phyml/20121109.patch) = 11016
@


1.2
log
@- Get Rid MD5 support
@
text
@d1 4
a4 2
SHA256 (phyml_20090706.tar.gz) = b39fa8ba2bc3a6566f3463c77db0d8992f71a71af353be539d0916173785d4bd
SIZE (phyml_20090706.tar.gz) = 818229
@


1.1
log
@PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide range of
options that were designed to facilitate standard phylogenetic analyses. The
main strengths of PhyML lies in the large number of substitution models coupled
to various options to search the space of phylogenetic tree topologies, going
from very fast and efficient methods to slower but generally more accurate
approaches. It also implements two methods to evaluate branch supports in a
sound statistical framework (the non-parametric bootstrap and the approximate
likelihood ratio test). PhyML was designed to process moderate to large data
sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long
can analyzed. In practice however, the amount of memory required to process a
data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided that
they are short. Also, PhyML can handle long sequences provided that they are
not numerous. With most standard personal computers, the "comfort zone" for
PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

WWW: http://code.google.com/p/phyml/

PR:		136877
Submitted by:	Ben Allen <ben@@sysadminschronicles.com>
@
text
@a0 1
MD5 (phyml_20090706.tar.gz) = 70e9963a04f5423124793467e8b50be0
@

