Multiple Sequence Alignments (MSAs) And Phylogenies - SOFTWARE

Contents:

• Pairwise Sequence Alignment
• Structural Alignment
• 3D Protein Structure Databases
• Resources/Databases providing pre-calculated Multiple Sequence Alignments
  
• Multiple Sequence Alignment Servers
• Multiple Sequence Alignment Reference Sets
• Locally Installed Software
• Other Protein Sequence Analysis Tools
• Phylogeny-Related Servers
  

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
  

Structural Alignment

• CE

3D Protein Structure Databases

• PDB

Resources/Databases providing pre-calculated Multiple Sequence Alignments

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

Multiple Sequence Alignment Servers

• clustalw
• tcoffee
• 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

Other Protein Sequence Analysis Tools

• ELM Resource for investigating linear protein motifs

Phylogeny-Related Servers

Databases/Resources exploring known trees

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

Phylogeny software

• RAxML webserver at CIPRES
• GBLOCKS