Results 10,751–10,760 of 19,819 for %22HTTP Server%22.(0.01 seconds)
Previous
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
Next
Object-oriented Perl API for the NEXUS file format
Bio::NEXUS package provides an object-oriented, Perl-based
applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on. This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).
Phylogenetic analysis using Perl
This is the base class for the Bio::Phylo package. All other modules
inherit from it, the methods defined here are applicable to all. Consult
the manual for usage examples: Bio::Phylo::Manual.
Read and Update SCF Chromatographic Sequence Files
Bio::SCF module allows you to read and update (in a restricted
way) SCF chromatographic sequence files. It is an interface to
Roger Staden's io-lib. See the installation directions for further
instructions.
Phylogeny Inference Package
PHYLIP (the PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). Methods that are available
in the package include parsimony, distance matrix, and likelihood
methods, including bootstrapping and consensus trees. Data types that
can be handled include molecular sequences, gene frequencies,
restriction sites, distance matrices, and 0/1 discrete characters.
Whole genome association analysis toolset
PLINK is a free, open-source whole genome association analysis toolset,
designed to perform a range of basic, large-scale analyses in a
computationally efficient manner.
Toolset for working with human genetic variation data
PLINK/SEQ is an open-source C/C++ library for working with human
genetic variation data. The specific focus is to provide a platform
for analytic tool development for variation data from large-scale
resequencing and genotyping projects, particularly whole-exome and
whole-genome studies. It is independent of (but designed to be
complementary to) the existing PLINK package.
Fast, memory-efficient, pythonic access to fasta sequence files
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.
Sequence assembler for very short reads
Velvet is a de novo genomic assembler specially designed for short read
sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
Citation:
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)
Generic nexus file format reader for python
python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)
reader for python.
Multiple DNA/protein sequence alignment editor
SeaView is a multiple sequence alignment editor.
You can align DNA/protein sequences from several organisms, and find
out their relative postions in phylogenic tree.
Once SeaView is installed, you can open the on-line help window through
the 'Help' button to learn how to use SeaView.
Example mase files can be found at:
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/