Links to Bioinformatics Software Resources

Contents:

Sites Listing Bioinformatics Resources

Multiple Sequence Alignments (MSAs) And Phylogenies - SOFTWARE

• Pairwise sequence alignment
• Pairwise 3D structural alignment
• 3D protein structure databases
• Resources/Databases providing pre-calculated multiple sequence alignments
  
• Multiple sequence alignment servers
• Multiple sequence alignment reference sets
• Software for local installation
  
• Phylogeny-related servers

Protein Modular Architecture Analysis

Bioinformatics Resource Listings

• Nucleic Acids Research (NAR) Webserver and Database collections
• Bioinformatics Links Directory
• ExPASY Life Science Directory and Proteomics Tools

Pairwise sequence alignment

• BLAST 2 Sequences at the NCBI
• Smith-Waterman/Needleman-Wunsch using EMBOSS at the EBI
• BLAST against sequence databases at NCBI
• BLAST against sequence databases at EBI
  

Pairwise 3D structural alignment

• CE
• FATCAT
  

3D Protein Structure Databases

• PDB at RSCB
• PDBsum
  

Resources/Databases providing pre-calculated multiple sequence alignments

• Ensembl (protein families)
• TreeFam
• PFAM
• HOMSTRAD
  

Multiple Sequence Alignment Servers

• CLUSTALW
• T_COFFEE
• MAFFT
• MUSCLE

Multiple Sequence Alignment Reference Sets

• BaliBase2
• BaliBase3

Locally Installed Software

Dendroscope (JAVA Phylogeny/Tree Viewer)

• Sofrware Download
• Article/Reference

NJPLOT

• Software Download

CLUSTALX

• Software Download

SEAVIEW

• Software Download

JALVIEW

• Software Download
• Documentation
• Hints on editing sequencnes

PyMOL

• Project Homepage
• Beginner's Tutorial
• Documentation
• Wiki

MESQUITE

• Project Hompage

Modular Protein Architecture Analysis

• UniProt
  
• PhosphoSite
• Human Protein Reference Database
• Phospho.ELM
• ELM Resource for investigating linear protein motifs

Simultaneous estimation of alignment and phylogeny

• StatAlign
• BAli-Phy
• SATCHMO (online webserver)
  
• SATe (not yet available)
  

Phylogeny-Related Servers

Databases/Resources exploring known trees

• TreeFam
• Tree of Life Project
• UCMP Tree of Life

Phylogeny software

• RAxML webserver at CIPRES
• GBLOCKS