| CATEGORY |
NAME |
DESCRIPTION |
PARALLEL |
| General |
EMBOSS 3.0.0 |
EMBOSS(European Molecular Biology Open Software Suite) is a suite of free software tools for sequence analysis. There are a wide variety of programs that make up the suite, ranging in application from database searching to presentation of sequence data. |
No |
| Alignment |
Clustalw 1.83 |
Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. |
No |
| MPI_Clustalw |
A parallel implementation of Clustal-W based on MPI . |
Yes |
| T-COFFEE |
A mulitple sequence alignemnt program |
No |
| GMAP |
Align and map cDNA , EST to genome database |
No |
| Search |
NCBI Blast |
Six versions of BLAST programs from NCBI, BioTeam, and others. We installed all the blast databases from NCBI and we also installed some other databases like dicty, arabidopsis, ceraptopsis databases (contact Luobin to install a database for your work). Luobin has also created "BlastFilter" to compile results for large, complicated BLAST jobs. |
Yes |
| mpiBLAST 1.3.0 |
MPI version of NCBI blast 2.2.10 |
Yes |
| Wise 2.2.0 |
Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence. |
No |
| Gene prediction |
GLIMMER 2.0 |
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. |
No |
| Phylogeny |
PHYLIP 3.6b |
PHYLIP is a free package of programs for inferring phylogenies |
No |
| PAUP 4b10 |
Phylogenetic Analysis Using Parsimony and other models. |
No |
| PAUPBOOT |
An MPI program to distribute PAUP bootstrap replicates to a cluster. |
Yes |
| MrBayes 3.12 |
MrBayes is a program for the Bayesian estimation of phylogeny. It is accessed throught command line interface. |
Yes |
| MrBayes 3.1.2 |
MrBayes is a program for the Bayesian estimation of phylogeny. It is accessed throught command line interface. |
Yes |
| PAML 3.14 |
PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. We added a web interface to the codeml program. |
No |
| fastDNAml |
fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. |
Yes |
| Tree-Puzzle 5.2 |
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood |
Yes |
| Molphy 2.3 |
MOLPHY is a program package for MOLecular PHYlogenetics |
No |
| Weighbor 1.2 |
Weighbor is a weighted version of Neighbor Joining that gives significantly less weight to the longer distances in the distance matrix. |
No |
| PhyML |
PhyML is a program to construct phylogeny using
maximum likelihood method. It is a very fast program compared to other maximum likelihood programs. |
No |
| ARB |
ARB |
ARB is an environment for 16s/18s/23s ribosomal RNA sequence data. It provides a windowing environment for building up databases of RNA sequences, aligning them, and searching, editing, modifying, aligning, profiling, and constructing trees. |
No |
| RNA |
Vienna RNA 1.5 |
Vienna RNA is a package for RNA secondary structure prediction and comparison |
No |
| Protein |
HMMER 2.3.2 |
HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. |
Yes |
| Predator 2.1.2 |
Predator is program to predict protein secondary structure from a single sequence or a set of sequences. |
No |
| Population |
Migrate 2.0.6 |
Migrate estimates effective population sizes and past migration rates between two or n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. |
Yes |
| LAMARC 2.0 |
Lamarc jointly estimates the population sizes, population growth rates, migration rates, recombination rate using a sample of sequence, SNP or microsatellite data. |
No |
| Structure 2.1 |
Structure is a program for using multi-locus genotype data to investigate population structure. Its uses include inferring the presense of distinct populations, assigning individuals to populations, sutdying higrid zones, identifying migrants and admixed individuals, and estimating population allele frquencies in situations where many individuals are migrants or admixed. |
No |
| Sequencing |
phred/phrap/consed |
Phred reads DNA sequencer trace data, calls bases, assigns quality
values to the bases, and writes the base calls and quality values to
output files. Phrap is a program for assembling shotgun DNA sequence data. |
No |
| CAP3 |
Contig Assembly Program |
No |
| RepeatMasker |
RepeatMasker |
No |
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