PHYLIP

From Wiki CEINGE

Revision as of 18:03, 12 June 2007 (edit) Mauro (Talk | contribs) (→PHYLIP) ← Previous diff		Revision as of 18:51, 12 June 2007 (edit) (undo) Mauro (Talk | contribs) (→PHYLIP) Next diff →
Line 1:		Line 1:
	==PHYLIP==		==PHYLIP==
-	PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies by using different methods, such as parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. It is able to accept different types of input data, such as molecular sequences, gene frequencies, restriction sites or distance matrices.	+
		+	===PHYLIP at CEINGE===
		+	PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies.
		+	At CEINGE, PHYLIP (verison 3.6) is installed and run on the cluster machine and is highly connected both with the Bioinformatic service and research group activity.
		+
		+	===Programs===
		+	The programs of Phylip packages use different methods, such as parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. It is able to accept different types of input data, such as molecular sequences, gene frequencies, restriction sites or distance matrices.
		+
		+	Some very ''popular'' programs are:
		+
		+	;'''PROTPARS''': estimates phylogenies from protein sequences using the parsimony method.
		+	;'''DNAPARS''': estimates phylogenies from DNA sequences using the parsimony method.
		+	;'''DNAML: estimates phylogenies from nucleotide sequences by maximum likelihood.
		+	;'''DNAMLK''': same as DNAML but assumes a molecular clock.
		+	;'''PROML''': estimates phylogenies from protein amino acid sequences by maximum likelihood.
		+	;'''PROMLK''': same as PROML but assumes a molecular clock.
		+	;'''FITCH''': estimates phylogenies from distance matrix data under the ''additive tree model'' according to which the distances are expected to equal the sums of branch lengths between the species.
		+	;'''KITSCH''':estimates phylogenies from distance matrix data under the ''ultrametric'' model which is the same as the additive tree model except that an evolutionary clock is assumed.
		+
		+	More information about PHYLIP package are available [http://bioinfo.ceinge.unina.it/help/phylip/ here]

---

Revision as of 18:51, 12 June 2007

PHYLIP

PHYLIP at CEINGE

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies. At CEINGE, PHYLIP (verison 3.6) is installed and run on the cluster machine and is highly connected both with the Bioinformatic service and research group activity.

Programs

The programs of Phylip packages use different methods, such as parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. It is able to accept different types of input data, such as molecular sequences, gene frequencies, restriction sites or distance matrices.

Some very popular programs are:

PROTPARS

estimates phylogenies from protein sequences using the parsimony method.

DNAPARS

estimates phylogenies from DNA sequences using the parsimony method.

DNAML: estimates phylogenies from nucleotide sequences by maximum likelihood.

DNAMLK

same as DNAML but assumes a molecular clock.

PROML

estimates phylogenies from protein amino acid sequences by maximum likelihood.

PROMLK

same as PROML but assumes a molecular clock.

FITCH

estimates phylogenies from distance matrix data under the additive tree model according to which the distances are expected to equal the sums of branch lengths between the species.

KITSCH

estimates phylogenies from distance matrix data under the ultrametric model which is the same as the additive tree model except that an evolutionary clock is assumed.

More information about PHYLIP package are available here