Our lab now uses PAUP*
One of the frustrating aspects of using phylogenetics software is the plethora of file formats. PAUP* uses the Nexus format, the popular PHYLIP format, the GCG molecular sequence analysis package uses the CGC format, and ClustalW uses its own format.
If you want to use more than one phylogenetic software to create alignments/phylogenetic analysis you need to know about all the formats. A quick table of some popular phylogenetic applications are listed below.
| NAME |
Description |
Methods |
Author |
| PHYLIP |
Phylogenetic inference package |
Maximum parsimony, distance matrix, maximum likelihood |
J. Felsenstein |
| PAUP |
Phylogenetic analysis using parsimony |
Maximum parsimony, distance matrix, maximum likelihood |
D. Swofford |
| PAML |
Phylogenetic analysis by maximum likelihood |
Maximum likelihood |
Z. Yang |
| ClustalW |
Progressive multiple sequence alignment |
Distance matrix/nearest neighbor |
Thompson et al. |
| QuickTree |
Tree construction optimized for efficiency |
Neighbor-joining |
K. Howe, A. Bateman, R. Durbin |
| MOLPHY |
Molecular phylogenetics (protein or nucleotide) |
Maximum likelihood |
J. Adachi and M. Hasegawa |
| TreeGen |
Tree construction given precomputed distance data |
Distance matrix |
ETH Zurich |
| fastDNAml |
Optimized maximum likelihood (nucleotides only) |
Maximum likelihood |
G.J. Olsen |
| TREE-PUZZLE |
Maximum likelihood and statistical analysis |
Maximum likelihood |
H.A. Schmidt, K. Strimmer, A. von Haeseler |
| TreeAlign |
Efficient hybrid method |
Distance matrix and approximate parsimony |
J. Hein |
| PhyloQuart |
Quartet implementation (uses sequences or distances) |
Quartet method |
V. Berry |
| MrBayes |
Posterior probability estimation |
Bayesian inference |
J. Huelsenbeck et al. |
