Task: Phylogeny
Metapackage: false
Description: Debian Med phylogeny packages
 This lists Debian packages related to phylogeny for use in life sciences.
 The purpose of this compilation of packages is to have a handy subset of
 from the med-bio metapackage which contains a lot more than only phylogeny
 related software.

Comment: Do not build a metapackage because it is not clear in how far this set of
 packages is complete regarding phylogeny.

X-Begin-Category: Phylogenetic analysis

Recommends: altree

Recommends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle

Recommends: probalign

Recommends: treeviewx

X-End-Category: Phylogenetic analysis

Recommends:     phylip
Why:         Phylogenetic analysis (Non-free, thus only suggested).

X-Comment: treetool is removed from Debian because it is not maintained upstream since
 1995 and cause the Xserver to freeze under Squeeze

X-Begin-Category: Sequence alignments and related programs.

Recommends:     muscle

Recommends: t-coffee

Recommends: kalign

Recommends: hmmer

Recommends: exonerate

Recommends: dialign

Recommends: dialign-tx

Recommends: poa

Recommends: probcons

Recommends: proda

Recommends: seaview

Recommends: sigma-align

Recommends: gmap

Recommends:     clustalx
Why:         Sequence alignments and related programs (Non-free, thus only suggested).

Recommends: clustalw

Recommends: mustang

X-End-Category: Sequence alignments and related programs.

X-Begin-Category: Models of nucleotide/amino acid evolution

Recommends: phyml

X-End-Category: Models of nucleotide/amino acid evolution

Recommends: beast-mcmc

Recommends: tm-align

Recommends: mrbayes

Recommends: figtree

Recommends: populations

X-Mark: Packages in Vcs - Information about these is queried from UDD as well

Recommends: proalign

Recommends: prottest

Recommends: treeview

Recommends: phylowin
Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html
WNPP: 395840
License: unknown
Pkg-Description: Graphical interface for molecular phylogenetic inference
 Phylo_win is a graphical colour interface for molecular phylogenetic
 inference. It performs neighbor-joining, parsimony and maximum
 likelihood methods and bootstrap with any of them. Many distances can be
 used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
 (1995), LogDet for nucleotidic sequences, Poisson correction for protein
 sequences, Ka and Ks for codon sequences. Species and sites to include
 in the analysis are selected by mouse. Reconstructed trees can be drawn,
 edited, printed, stored and evaluated according to numerous criteria.
 .
 This program uses sources files from the Phylip program, which forbids
 its use for profit.  Therfore, Phylo_win will unfortunately have to be
 distributed in contrib or non-free.
Remark: Issuer of previous ITP said:
 Because I could never figure out the license of Phylo_win, and because the
 upstream authors released SeaView 4, which provides similar functionalities, I
 will not package Phylo_win.
 .
 Probably it makes sense to remove this project from the prospective packages
 list.


Recommends: gbioseq
Homepage: http://www.bioinformatics.org/project/?group_id=94
License: GPL
Pkg-Description: DNA sequence editor for Linux
 gBioSeq is in an early stage of development, but it is already running.
 The goal is to provide an easy to use software to edit DNA sequences under
 Linux, Windows, MacOsX, using GTK C# (Mono).

Recommends: phpphylotree
Homepage: http://www.bioinformatics.org/project/?group_id=372
License: GPL
Pkg-Description: draw phylogenetic trees
 PhpPhylotree is a web application that is able to draw phylogenetic trees.
 It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.

Recommends: jstreeview
Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml
License: MIT/X11
Language: JavaScript
Pkg-Description: Editor for Phylogenetic Trees
 A concise viewer/editor for phylogenetic trees in the Newick format.
 The core functions are written in JavaScript, using the canvas tag
 proposed by HTML 5. No server side support is needed for rendering the
 picture and therefore you can grab this page together with knhx.js and
 canvastext.js to locally view your trees in a supported web browser.
 .
 The source can be downloaded at
 http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip

Recommends: treetime
Homepage: http://treetime.linhi.com/
License: GPL
Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data
 TreeTime is controlled by input files in nexus format and does
 bayesian sampling of phylogenetic trees from these data.

Recommends: jmodeltest

Recommends: forester

Recommends: patristic
Language: Java

Recommends: spread-phy

Recommends: iqtree

Suggests: python3-treetime

Recommends: pplacer

Recommends: quicktree
