Phylogenetic programs

List of phylogenetic packages and free servers (PHYLIP pages)

PHYLIP

Server for phylogenetic analysis using the PHYLIP package

BIONJ

Server for Neighbour Joining phylogenetic analysis

TREE PUZZLE

 Package for phylogenetic analysis by Maximum Likelihood

PHYML

 Server for Maximum Llikehood phylogenetic analysis 

SAPS

Statistical analysis of protein sequences at EMBnet-CH

 FastPCR

Excellent free downloadable PCR primer design software and can design primers for standard and long PCR, inverse PCR, degenerate PCR directly on amino acid sequence, multiplex PCR

Electronic PCR

Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites(STSs), within DNA sequences.

Primer 3

Selects PCR primers from nucleotide sequences

PrimerQuest

Tool for the design of PCR primers, probes, and sequencing primers

 Primer Design Assistant (PDA) 

 A web-based primer design tool

 MethPrimer

 Design Primers for Methylation PCRs. The only free public methylation primer program available.

AutoPrime

Freely accessible web-based primer design software which designs primers of high quality for Real-Time-Quantitative PCR 

WebCutter

Web-based tool for restriction mapping of DNA sequences

NEBcutter V.2.0     

For all Type II and commercially available Type III restriction enzymes that cut the sequence just once