LAMARC (Likelihood Analysis with Metropolis Algorithm using Random
Coalescence) is a package of programs for computing population parameters
such as population size, population growth rate and migration rates. It does
this by using likelihoods for samples of data (sequences, microsatellites,
and electrophoretic polymorphisms) from populations.
Phylogenetic Analysis by Maximum Likelihood (PAML)
PAML is a package of programs for phylogenetic analyses of DNA or protein
sequences using maximum likelihood. It is not good for tree making. It may be
used to estimate parameters and test hypotheses for the study the evolutionary
process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
PhyML, or RaxML.
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.
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.
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
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/
TreeView X is program to display phylogenetic trees on Unix-like platforms.
It can read and display NEXUS and Newick format tree files (such as those
output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It has a
subset of the functionality of the version of TreeView available for the
Mac Classic and Windows (it is roughly equivalent to version 0.95 of
TreeView).
dxf2fig parses Autocad DXF input, then calls external routines to do either
plotting or a fig conversion for xfig. The conversion is fairly complete.
Layers (depths in xfig), blocks (compounds in xfig), colors, and linetypes
are roughly preserved in the output file.
gSpiceUI is intended to provide a GUI for freely available electronic
circuit simulation engines ie. NG-Spice and GNU-Cap. The utility gnetlist is
used to convert schematic files to netlist files, Gwave or Gaw to display
simulation results and gschem is the preferred schematic capture tool.
MeshLab is an open source, portable, and extensible system for the processing
and editing of unstructured 3D triangular meshes. The system is aimed to help
the processing of the typical not-so-small unstructured models arising in 3D
scanning, providing a set of tools for editing, cleaning, healing, inspecting,
rendering and converting this kind of meshes.