PHYLIP - Revision history

Leandra at 10:38, 22 June 2007

2007-06-22T10:38:03Z

←Older revision		Revision as of 10:38, 22 June 2007
Line 3:		Line 3:

	===How to reach PHYLIP===		===How to reach PHYLIP===
-	:PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it ~~Bioinfo~~ website] through the [[PROGsDB]].	+	:PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it main website] or through the [[PROGsDB]]..
	:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].		:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].
	:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.		:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.
Line 10:		Line 10:
	: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.		: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:	+	:Some frequently used programs are:
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.
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	===References===		===References===
-
	:Felsenstein, J '''PHYLIP -- Phylogeny Inference Package (Version 3.2)''', ''Cladistics'' 5: 164-166, 1989.		:Felsenstein, J '''PHYLIP -- Phylogeny Inference Package (Version 3.2)''', ''Cladistics'' 5: 164-166, 1989.

-	:For ~~more~~ details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]	+	:For further details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]

	{{footer\|footername=footer bioinfo}}		{{footer\|footername=footer bioinfo}}

Giovanni at 06:46, 22 June 2007

2007-06-22T06:46:34Z

←Older revision		Revision as of 06:46, 22 June 2007
Line 25:		Line 25:
	:For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]		:For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]

-	{{footer bioinfo}}	+	{{footer\|footername=footer bioinfo}}

Giovanni at 15:49, 20 June 2007

2007-06-20T15:49:51Z

←Older revision		Revision as of 15:49, 20 June 2007
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	:For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]		:For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]
		+
		+	{{footer bioinfo}}

Mauro at 11:18, 20 June 2007

2007-06-20T11:18:01Z

←Older revision		Revision as of 11:18, 20 June 2007
Line 6:		Line 6:
	:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].		:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].
	:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.		:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.
-

	===Available programs===		===Available programs===
Line 12:		Line 11:

	:Some very ''popular'' programs are:		:Some very ''popular'' programs are:
-
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.

Mauro at 11:17, 20 June 2007

2007-06-20T11:17:32Z

←Older revision		Revision as of 11:17, 20 June 2007
Line 15:		Line 15:
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.
-	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnaml.php DNAML]''': estimates phylogenies from nucleotide sequences by maximum likelihood.
-	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnamlk.php DNAMLK]''': same as DNAML but assumes a molecular clock.
-	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/proml.php PROML]''': estimates phylogenies from protein amino acid sequences by maximum likelihood.
-	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/promlk.php PROMLK]''': same as PROML but assumes a molecular clock.
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/fitch.php 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.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/fitch.php 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.
	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/kitsch.php 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.		:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/kitsch.php 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.

Mauro at 11:15, 20 June 2007

2007-06-20T11:15:58Z

←Older revision		Revision as of 11:15, 20 June 2007
Line 13:		Line 13:
	:Some very ''popular'' programs are:		:Some very ''popular'' programs are:

-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/dnaml.php DNAML]''': estimates phylogenies from nucleotide sequences by maximum likelihood.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnaml.php DNAML]''': estimates phylogenies from nucleotide sequences by maximum likelihood.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/dnamlk.php DNAMLK]''': same as DNAML but assumes a molecular clock.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnamlk.php DNAMLK]''': same as DNAML but assumes a molecular clock.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/proml.php PROML]''': estimates phylogenies from protein amino acid sequences by maximum likelihood.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/proml.php PROML]''': estimates phylogenies from protein amino acid sequences by maximum likelihood.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/promlk.php PROMLK]''': same as PROML but assumes a molecular clock.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/promlk.php PROMLK]''': same as PROML but assumes a molecular clock.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/fitch.php 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.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/fitch.php 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.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/kitsch.php 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.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/kitsch.php 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.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/drawgram.php DRAWGRAM]''': plots rooted phylogenies, cladograms, circular trees and phenograms.	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/drawgram.php DRAWGRAM]''': plots rooted phylogenies, cladograms, circular trees and phenograms.
-	:*'''[http://bioinfo.ceinge.unina.it/~~tolls~~/winterf/drawtree.php DRAWTREE]''': similar to DRAWGRAM but plots unrooted phylogenies.[	+	:*'''[http://bioinfo.ceinge.unina.it/tools/winterf/drawtree.php DRAWTREE]''': similar to DRAWGRAM but plots unrooted phylogenies.
	:A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here]		:A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here]

Mauro at 11:14, 20 June 2007

2007-06-20T11:14:31Z

←Older revision		Revision as of 11:14, 20 June 2007
Line 13:		Line 13:
	:Some very ''popular'' programs are:		:Some very ''popular'' programs are:

-	:*'''PROTPARS''': estimates phylogenies from protein sequences using the parsimony method.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method.
-	:*'''DNAPARS''': estimates phylogenies from DNA sequences using the parsimony method.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method.
-	:*'''DNAML''': estimates phylogenies from nucleotide sequences by maximum likelihood.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/dnaml.php DNAML]''': estimates phylogenies from nucleotide sequences by maximum likelihood.
-	:*'''DNAMLK''': same as DNAML but assumes a molecular clock.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/dnamlk.php DNAMLK]''': same as DNAML but assumes a molecular clock.
-	:*'''PROML''': estimates phylogenies from protein amino acid sequences by maximum likelihood.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/proml.php PROML]''': estimates phylogenies from protein amino acid sequences by maximum likelihood.
-	:*'''PROMLK''': same as PROML but assumes a molecular clock.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/promlk.php 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.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/fitch.php 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.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/kitsch.php 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.
-	:*'''DRAWGRAM''': plots rooted phylogenies, cladograms, circular trees and phenograms.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/drawgram.php DRAWGRAM]''': plots rooted phylogenies, cladograms, circular trees and phenograms.
-	:*'''DRAWTREE''': similar to DRAWGRAM but plots unrooted phylogenies.	+	:*'''[http://bioinfo.ceinge.unina.it/tolls/winterf/drawtree.php DRAWTREE]''': similar to DRAWGRAM but plots unrooted phylogenies.[
-		+
	:A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here]		:A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here]

Mauro at 11:10, 20 June 2007

2007-06-20T11:10:41Z

←Older revision		Revision as of 11:10, 20 June 2007
Line 4:		Line 4:
	===How to reach PHYLIP===		===How to reach PHYLIP===
	:PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].		:PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].
-
	:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].		:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].
-
	:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.		:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.

Mauro at 11:10, 20 June 2007

2007-06-20T11:10:16Z

←Older revision		Revision as of 11:10, 20 June 2007
Line 1:		Line 1:
-	:PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies.	+	PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies.
-	:PHYLIP (verison 3.6) is installed and run on the cluster server and is highly connected both with the Bioinformatic service and research group activity. For example, they are used to define relationships among conserved sequences in different species in evolutionary analyses.	+	PHYLIP (verison 3.6) is installed and run on the cluster server and is highly connected both with the Bioinformatic service and research group activity. For example, they are used to define relationships among conserved sequences in different species in evolutionary analyses.

	===How to reach PHYLIP===		===How to reach PHYLIP===

Mauro at 11:09, 20 June 2007

2007-06-20T11:09:53Z

←Older revision		Revision as of 11:09, 20 June 2007
Line 1:		Line 1:
-	PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies.	+	: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.	+	:PHYLIP (verison 3.6) is installed and run on the cluster server and is highly connected both with the Bioinformatic service and research group activity. For example, they are used to define relationships among conserved sequences in different species in evolutionary analyses.

-	===~~Programs~~===	+	===How to reach PHYLIP===
-	~~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~~.	+	:PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].

-	Some ~~very ''popular'' programs are:~~	+	:Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by [[CAPRI]].
-		+
-	*'''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.~~	+
-	*'''DRAWGRAM~~''': plots rooted phylogenies, cladograms, circular trees~~ and ~~phenograms.~~	+
-	*'''DRAWTREE~~''': similar to DRAWGRAM but plots unrooted phylogenies~~.	+

-	~~A detailed explanation of all~~ PHYLIP ~~programs~~ is available ~~[http:~~//~~bioinfo~~.~~ceinge.unina.it/help/phylip/ here]~~	+	:In the [[VLS]] environment, the PHYLIP package is fully available for command line use in the directory ''/bioprogs/phylip''.

-	===How to reach and use PHYLIP===
-	PHYLIP programs can be searched and launched from the [http://bioinfo.ceinge.unina.it Bioinfo website] through the [[PROGsDB]].

-	~~Some~~ of ~~the application~~, such as DRAWGRAM and DRAWTREE ~~can be directly launched by [[CAPRI]]~~.	+	===Available 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.
		+	:*'''DRAWGRAM''': plots rooted phylogenies, cladograms, circular trees and phenograms.
		+	:*'''DRAWTREE''': similar to DRAWGRAM but plots unrooted phylogenies.

-	~~In the [[VLS]] environment, the~~ PHYLIP ~~package~~ is ~~fully~~ available ~~for command line use in the directory ''~~/~~bioprogs~~/~~phylip''~~.	+	:A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here]

-	=== References ===	+	===References===

-	Felsenstein, J '''PHYLIP -- Phylogeny Inference Package (Version 3.2)''', ''Cladistics'' 5: 164-166, 1989.	+	:Felsenstein, J '''PHYLIP -- Phylogeny Inference Package (Version 3.2)''', ''Cladistics'' 5: 164-166, 1989.

-	For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]	+	:For more details about PHYLIP, visit the [http://evolution.genetics.washington.edu/phylip.html PHYLIP web site]