Ubuntu
phyml package

phyml 3:3.3.20211021-1 source package in Ubuntu

Changelog

phyml (3:3.3.20211021-1) unstable; urgency=medium

  * New upstream version.
  * Refresh most patches.
  * Add apply-cflags.patch: ensure standard Debian CFLAGS are propagated
    throughout the build process.
  * Add filter-sse3-intrinsics.patch: fixes FTBFS when built with -msse but
    without -msse3, as the codebase also now includes SSE3 instructions;
    however this means that SSE acceleration is thus now disabled on amd64.
  * Add apply-ldflags.patch: ensure standard Debian LDFLAGS are propagated
    throughout the build process for proper hardening.
  * d/rules: autoconfigure with --enable-phyml-mpi, replacing --enable-mpi.
  * d/rules: fix permissions of example files nucleic and proteic.
  * d/{links,phyml.1}: also provide phyml-mpi manual page.
  * d/control: add myself to Uploaders.
  * d/copyright: bump project to GPL-3 and document the file src/mxml.h
  * d/copyright: update copyright entry of package maintenance

 -- Étienne Mollier <email address hidden>  Fri, 19 Nov 2021 00:22:37 +0100

Upload details

Uploaded by:
Debian Med
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
any
Section:
science
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section

Downloads

File Size SHA-256 Checksum
phyml_3.3.20211021-1.dsc 2.1 KiB d44bcec424bb82635a01b9c4a152e86f3bb1cc0182b6131b284ad2a4c26068eb
phyml_3.3.20211021.orig.tar.gz 1.7 MiB 8dd6519ccbf73ce67e57bc7681f6dffdbbc63e78e15aae79394f3ec362d42c2d
phyml_3.3.20211021-1.debian.tar.xz 20.1 KiB d0742cebf4095013bd842a69f75c30a915d46445f16000733ccc7293aa0e2194

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Binary packages built by this source

phyml: Phylogenetic estimation using Maximum Likelihood

 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
 be 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.
 .
 This package also includes PhyTime.

phyml-dbgsym: debug symbols for phyml