[Blends-commit] r2680 - /projects/med/trunk/debian-med/tasks/bio-phylogeny

Thu Feb 17 15:29:28 UTC 2011

Author: tille
Date: Thu Feb 17 15:29:23 2011
New Revision: 2680

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2680
Log:
Add another slice of biological software in a separate metapackage - not sure whether this will remain for the future

Added:
    projects/med/trunk/debian-med/tasks/bio-phylogeny

Added: projects/med/trunk/debian-med/tasks/bio-phylogeny
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-phylogeny?rev=2680&op=file
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio-phylogeny (added)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Thu Feb 17 15:29:23 2011
@@ -1,0 +1,402 @@
+Task: Phylogeny
+Description: Debian Med phylogeny packages
+ This metapackage will install Debian packages related to phylogeny for
+ use in life sciences.
+
+X-Begin-Category: Phylogenetic analysis
+
+Depends: altree
+Remark: altree 1.1.0 should be not be packaged
+ According to Vincent Danjean <vdanjean.ml at 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 at 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 at 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 at 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: populations
+Homepage: http://bioinformatics.org/~tryphon/populations/
+License: GPL
+Pkg-Description: individuals or populations distances based on allelic frequencies
+ Population genetic software (individuals or populations distances, phylogenetic trees)
+  * haploids, diploids or polyploids genotypes (see input formats)
+  * structured populations (see input files structured populations
+  * No limit of populations, loci, alleles per loci (see input formats)
+  * Distances between individuals (15 different methods)
+  * Distances between populations (15 methods)
+  * Bootstraps on loci OR individuals
+  * Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA
+    (PHYLIP tree format)
+  * Allelic diversity
+  * Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
+    Populations...)
+
+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 at 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
+Homepage: http://mrbayes.csit.fsu.edu/
+License: GPL
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/
+Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Bayesian estimation of phylogeny
+ MrBayes is a program for the Bayesian estimation of
+ phylogeny. Bayesian inference of phylogeny is based upon a quantity
+ called the posterior probability distribution of trees, which is the
+ probability of a tree conditioned on the observations. The
+ conditioning is accomplished using Bayes's theorem. The posterior
+ probability distribution of trees is impossible to calculate
+ analytically; instead, MrBayes uses a simulation technique called
+ Markov chain Monte Carlo (or MCMC) to approximate the posterior
+ probabilities of trees.
+ .
+ The program takes as input a character matrix in a NEXUS file
+ format. The output is several files with the parameters that were
+ sampled by the MCMC algorithm. MrBayes can summarize the information
+ in these files for the user. The program features include:
+Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
+
+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: figtree
+Homepage: http://tree.bio.ed.ac.uk/software/figtree/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/figtree/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/figtree/trunk/?rev=0&sc=0
+License: GPL
+Language: Java
+Pkg-Description: graphical phylogenetic tree viewer
+ FigTree is designed as a graphical viewer of phylogenetic trees and as
+ a program for producing publication-ready figures.  In particular it is
+ designed to display summarized and annotated trees produced by BEAST.
+
+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/


