Programs For Biology 3S03

Chapter 1 Preliminaries

Chapter 2 Genomics

Chapter 3 Unix Basics

Chapter 4 Databases

Chapter 5 Sequence File Formats

Chapter 6 Database Searching

Chapter 7 Sequence Alignment

align [ align.doc] [ get your own copy]

Compute a global alignment of two sequences.

align0 [ align0.doc] [ get your own copy]

Compute a global alignment of two sequences without penalizing for end_gaps.

lalign [ lalign.doc ] [ get your own copy]

Find the best local alignments between two sequences.

clustalw [ advanced form ] [ clustalw.doc] [ get your own copy]

muscle [ advanced form ]

Multiple Alignments Computation.

prss [ prss.doc] [ get your own copy]

Compare a test sequence to a shuffled sequence.

prdf [ prdf.doc] [ get your own copy]

Compare a test sequence to a shuffled sequence.

Chapter 8 Distance Measures

dnadist [ advanced form ] [ dnadist.doc ] [ get your own copy]

Distances from DNA sequences.

Most instances of the PHYLIP interleaved format work fine in the dnadist program. However, if in the result page you get a listing indicating that your input data is different from your original data then

please go to the Chapter 5 section and run the fmtseq program to transfer your original data into PHYLIP sequential format, and then run dnadist again.

protdist [ advanced form ] [ protdist.doc] [ get your own copy]

Distances from protein sequences.

Chapter 9 Reconstructing Phylogenies

dnapars [ advanced form ] [ dnapars.doc [ get your own copy]

Parsimony method for DNA.

dnaml [ get your own copy]

(Maximum likelihood method) has been removed.; please use rather fastDNAml [advanced form], which is much faster and equivalent.

protpars [advanced form ] [protpars.doc] [ get your own copy]

Parsimony method for protein sequences.

neighbor [ advanced form ] [ neighbor.doc] [ get your own copy]

Neighbor-joining and UPGMA methods

fitch [ advanced form [ fitch.doc [ get your own copy]

Fitch-Margoliash and least-squares methods

kitsch [ advanced form ] [ kitsch.doc ] [ get your own copy]

Fitch-Margoliash and least-squares methods with molecular clock

consense [ advanced form ] [ consense.doc ] [ get your own copy]

Consensus tree program

dollop [ advanced form] [ dollop.doc] [ get your own copy]

Dollop and Polymorphism Parsimony Program

pars [ advanced form ] [ pars.doc] [ get your own copy]

Discrete character parsimony

puzzle [ advanced form ] [ puzzle.doc ] [ get your own copy]

Tree reconstruction for sequences by quartet puzzling and maximum likelihood

Chapter 10 Pattern Analysis

Chapter 11 Exon Analysis

Miscellaneous

drawtree [ advanced form ] [ drawtree.doc] [ get your own copy]

Draw a tree (as computed before by phylogenetic analysis methods).

drawgram [ advanced form ] [ drawgram.doc] [ get your own copy]

Draw a phenogram (see comment for drawtree)

unroot [ get your own copy]

Unroot a tree with the retree.doc program.

clique [ advanced form ] [ clique.doc ] [ get your own copy]

Compatibility Program

mix [ advanced form] [ mix.doc [ get your own copy]

Mixed method parsimony

Web Access to EMBOSS

The European Molecular Biology Open Software Suite

Pasteur Inst

A Galaxy web portal from the Pasteur Inst