Development has been discontinued more than one year
> Revision 1.354: download - view: text, markup, annotated - select for diffs
> Wed Mar 12 23:27:09 2008 UTC (16 months, 1 week ago) by maho
See also PR: 136674
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>
1. Add a $FreeBSD Id
2. Remove the spurious FreeBSD KEYWORD
3. s#/etc/rc.subr#%%RC_SUBR%%#
4. s#/usr/local#%%PREFIX%%#
5. Move load_rc_config to after the method definition and move
the default _enable assignment after it.
6. The _stop method was a less efficient version of the default, so remove it
1. Change default variable assignments at the top to comments (two of
them were assigning empty default values).
2. Move the default for _enable to below load_rc_config
3. Add the _ifaces and _server options to command_args which eliminates
the need for the precmd
4. s#/usr/local#%%PREFIX%%#
o Fix not real world communications via gen_eth (FreeBSD's libpcap) issue.
o Take MAINTAINERship to myself.
o Bump PORTREVISION accordingly.
Approved by: fjoe (maintainer)
- Use openssl from ports for older FreeBSD versions
- Add a patch to handle openssl errors properly
- While here, fix building with custom PREFIX/LOCALBASE
PR: 136793
Submitted by: Andrew Lewis <freeghb@gmail.com> (maintainer)
