PHYLIP

PHYLIP, which stands for "The PHYLogeny Inference Package, is a collection of applications that were developed to help advanced computer users such as genetics engineers or scientists in related fields infer evolutionary trees (phylogenies).

Among the methods that can be found in the package you can find parsimony, likelihood methods such as bootstrapping and consensus trees, as well as distance matrix.

The types of data that can be handled by these applications include gene frequencies, distance matrices, molecular sentences, restriction sites and fragments and discrete characters.

The tools can be easily controlled via a menu, which prompts the user to configure the options beforehand and then enables them to start computing the data. Information is accessed by the program from a text document on the computer, which can be prepared in advance by using any text editor or word processor.

It is worth mentioning that in order to use text documents from the PC, users must save them as flast ASCII or Text Only formats, as proprietary formats don't work at all when you try to import them.

Some programs are able to write data files in the PHYLIP format. Most of the tools attempt to identify data in a document called "infile." In case this document is not found, they prompt the user to type the name of the data file manually.