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

Depends: altree
Remark: altree 1.1.0 should be not be packaged
 According to Vincent Danjean <vdanjean.ml@free.fr> version 1.1.0 should not
 be packaged for two reasons:
 .
  1. New dependencies (libtamuanova-perl, nanova and libnanova-perl) which
     need to be packaged.
  2. There are still bugs in the new method added in altree 1.1.0 and the doc
     is not updated.
 .
 See http://lists.debian.org/debian-med/2009/08/msg00104.html for further
 details.

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

Depends: probalign

Depends: treeviewx
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: Computer Applications in the Bioscience 12:357-358
Published-Year: 1996

X-End-Category: Phylogenetic analysis

Depends:     molphy, 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.

Depends:     muscle

Depends: t-coffee
Published-Title: T-Coffee: A novel method for multiple sequence alignments
Published-Authors: C. Notredame, D. Higgins, J. Heringa
Published-In: Journal of Molecular Biology 302(1):205-217
Published-Year: 2000
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
Published-PubMed: 10964570

Depends: kalign
Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
Published-Authors: Lassmann T, Sonnhammer EL.
Published-In: BMC Bioinformatics, 6:298
Published-Year: 2005
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16343337
Published-PubMed: 16343337

Depends: hmmer
Published-Title: Multiple Alignment Using Hidden Markov Models.
Published-Authors: S. R. Eddy.
Published-In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
Published-Year: 1995
Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf

Depends: exonerate
Published-Title: Automated generation of heuristics for biological sequence comparison
Published-Authors: G.C. Slater, E. Birney
Published-In: BMC Bioinformatics 6:31
Published-Year: 2005
Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
Published-doi: 10.1186/1471-2105-6-31

Depends: dialign
Published-Authors: Burkhard Morgenstern
Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Published-In: Bioinformatics 15(3):211-218
Published-Year: 1999
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408

Depends: dialign-tx
Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
Published-In: Algorithms for Molecular Biology 3:6
Published-Year: 2008
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568

Depends: poa
Published-Authors: C. Grasso, C. Lee
Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Published-In: Bioinformatics 20(10):1546-1556.
Published-Year: 2004

Depends: probcons
Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
Published-In: Genome Research 15: 330-340
Published-Year: 2005

Depends: proda
Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
Published-In: Nucleic Acids Research 34(20), 5932-5942
Published-Year: 2006

Depends: seaview
Published-Authors: N. Galtier, M. Gouy, C. Gautier
Published-Title: SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny
Published-In: Comput. Applic. Biosci. 12:543-548
Published-Year: 1996

Depends: sigma-align
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: BMC Bioinformatics 16;7:143
Published-Year: 2006

Depends: gmap
Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Published-Authors: Thomas D. Wu, Colin K. Watanabe
Published-In: Bioinformatics
Published-Year: 2005
Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859

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

Depends: clustalw
Published-Authors: M. Larkin, et al.
Published-Title: Clustal W and Clustal X version 2.0
Published-In: Bioinformatics 23(21):2947-2948
Published-Year: 2007

Depends: clustalw-mpi
Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
 not possible to specify an "OR relation" and tag the Published-* fields to only one
 of them.

Depends: mustang
Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
Published-Title: MUSTANG: A multiple structural alignment algorithm
Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
Published-Year: 2006

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

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

Depends: phyml

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


Depends: jtreeview
Homepage: http://jtreeview.sourceforge.net/
Responsible: Steffen Moeller <moeller@debian.org>
License: GPL
WNPP: 243771
X-Category: Visualisation
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/treeview/trunk/
Pkg-Description: Java re-implementation of Michael Eisen's TreeView
 TreeView creates a matrix-like display of expression data, known as
 Eisen clustering. The original implementation was a Windows program
 named TreeView by Michael Eisen. This TreeView package, sometimes also
 referred to as jTreeView, was rewritten in Java under a free license,
 the original implementation also comes with the source code, but controls
 commercial distribution. And it did not run on Unix.
 .
 Java TreeView is an extensible viewer for microarray data in
 PCL or CDT format.

Depends: proalign
Homepage: http://evol-linux1.ulb.ac.be/ueg/ProAlign/
License: GPL
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 378290
Pkg-Description: Probabilistic multiple alignment program
 ProAlign performs probabilistic sequence alignments using hidden Markov
 models (HMM). It includes a graphical interface (GUI) allowing to (i)
 perform alignments of nucleotide or amino-acid sequences, (ii) view the
 quality of solutions, (iii) filter the unreliable alignment regions and
 (iv) export alignments to other softwares.
 .
 ProAlign uses a progressive method, such that multiple alignment is
 created stepwise by performing pairwise alignments in the nodes of a
 guide tree. Sequences are described with vectors of character
 probabilities, and each pairwise alignment reconstructs the ancestral
 (parent) sequence by computing the probabilities of different
 characters according to an evolutionary model. It has been published in
 Bioinformatics. 2003 Aug 12;19(12):1505-13.

Depends: tm-align

Depends: phylographer
Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
Responsible: Charles Plessy <plessy@debian.org>
WNPP: 426489
License: GPL
X-Category: Graphical representation of sequence conservation
Language: Tcl/Tk
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phylographer/trunk/
Pkg-Description: Graph Visualization Tool
 PhyloGrapher is a program designed to visualize and study evolutionary
 relationships within families of homologous genes or proteins
 (elements).  PhyloGrapher is a drawing tool that generates custom graphs
 for a given set of elements. In general, it is possible to use
 PhyloGrapher to visualize any type of relations between elements.
 Used in conjunction with tcl_blast_parser, PhyloGrapher can represent
 the results of a BLAST search as a graph.
 .
 PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST
 biological sequence alignment reports (BLAST is provided by Debian's
 blast2 package).

Depends: 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.


Depends: 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).

Depends: 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.

Depends: beast-mcmc
Homepage: http://beast.bio.ed.ac.uk/
License: LGPL
WNPP: 552101
Responsible: Felix Feyertag <felix.feyertag@gmail.com>
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/
Pkg-Description: Bayesian MCMC analysis of molecular sequences
 BEAST is a cross-platform program for Bayesian MCMC analysis of
 molecular sequences.  It is entirely orientated towards rooted,
 time-measured phylogenies inferred using strict or relaxed molecular
 clock models. It can be used as a method of reconstructing
 phylogenies but is also a framework for testing evolutionary
 hypotheses without conditioning on a single tree topology. BEAST uses
 MCMC to average over tree space, so that each tree is weighted
 proportional to its posterior probability. We include a simple to use
 user-interface program for setting up standard analyses and a suit of
 programs for analysing the results.
 .
 The source is avialable at http://code.google.com/p/beast-mcmc/ .
Published-Title: BEAST: Bayesian evolutionary analysis by sampling trees
Published-Authors: A. J. Drummond, A. Rambaut
Published-In: BMC Evolutionary Biology
Published-Year: 2007
Published-URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
Published-DOI: 10.1186/1471-2148-7-214
Published-PubMed: 17996036

Depends: mrbayes

Depends: figtree

Depends: populations

Depends: 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

Depends: 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.

Depends: jmodeltest
Homepage: http://darwin.uvigo.es/software/jmodeltest.html
License: GPL
Pkg-Description: phylogenetic model averaging
 JModelTest is a tool to carry out statistical selection of best-fit
 models of nucleotide substitution. It implements five different model
 selection strategies: hierarchical and dynamical likelihood ratio tests
 (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC),
 and a decision theory method (DT). It also provides estimates of model
 selection uncertainty, parameter importances and model-averaged
 parameter estimates, including model-averaged phylogenies. Please note
 that the DT weights are very gross 

Depends: prottest
License: GPL, MIT
Homepage: http://darwin.uvigo.es/software/prottest.html
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/prottest/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/prottest/trunk/
Pkg-Description: Selection of best-fit models of protein evolution
 PROTTEST (ModelTest's relative) is a program for selecting the model of
 protein evolution that best fits a given set of sequences (alignment).
 This java program is based on the Phyml program (for maximum likelihood
 calculations and optimization of parameters) and uses the PAL library as
 well. Models included are empirical substitution matrices (such as WAG,
 LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
 MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
 replacement, and specific improvements (+I:invariable sites, +G: rate
 heterogeneity among sites, +F: observed amino acid frequencies) to
 account for the evolutionary constraints impossed by conservation of
 protein structure and function. ProtTest uses the Akaike Information
 Criterion (AIC) and other statistics (AICc and BIC) to find which of the
 candidate models best fits the data at hand.

Depends: patristic
License: GPL3
Homepage: ftp://ftp.bioinformatics.org/pub/patristic/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/patristic/trunk
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/patristic/trunk/?rev=0&sc=0
Language: Java
Pkg-Description: Calculate patristic distances and comparing the components of genetic change
 Patristic overcomes some logistic barriers to analysing signals in
 sequences. In additional to calculating patristic distances, it provides
 plots for any combination of matrices, calculates commonly used
 statistics, allows data such as isolation dates to be entered and
 reorders matrices with matching species or gene labels. It will be used
 to analyse rates of mutation and substitutional saturation and the
 evolution of viruses.
Published-URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1352388/
