[Seqinr-commits] r1749 - pkg/man

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2010-08-25 14:44:39 +0200 (Wed, 25 Aug 2010)
New Revision: 1749

Added:
   pkg/man/clustal.Rd
   pkg/man/fasta.Rd
   pkg/man/mase.Rd
   pkg/man/msf.Rd
   pkg/man/phylip.Rd
Log:
Addition of documentation for alignment formats datasets


Added: pkg/man/clustal.Rd
===================================================================
--- pkg/man/clustal.Rd	                        (rev 0)
+++ pkg/man/clustal.Rd	2010-08-25 12:44:39 UTC (rev 1749)
@@ -0,0 +1,13 @@
+\name{clustal}
+     \docType{data}
+     \alias{clustal}
+     \title{Example of results obtained after a call to read.alignment}
+     \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "clustal" format.}
+     \usage{clustal}
+     \format{A List of class alignment}
+     \source{http://www.clustal.org/}
+     \references{
+      Thompson, J.D., Higgins D.G., Gibson T.J. (1994) \emph{CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice}.
+      Nucleic Acids Res. 22(22):4673-80.
+     }
+     \keyword{datasets}

Added: pkg/man/fasta.Rd
===================================================================
--- pkg/man/fasta.Rd	                        (rev 0)
+++ pkg/man/fasta.Rd	2010-08-25 12:44:39 UTC (rev 1749)
@@ -0,0 +1,10 @@
+\name{fasta}
+     \docType{fasta}
+     \alias{fasta}
+     \title{Example of results obtained after a call to read.alignment}
+     \description{This data set gives an example of a amino acids alignment obtained after a call to the function read.alignment on an alignment file in "fasta" format.}
+     \usage{fasta}
+     \format{A List of class alignment}
+     \source{http://pbil.univ-lyon1.fr/help/formats.html/}
+     \references{Pearson W.R. and Lipman D.J. (1988) \emph{Improved tools for biological sequence comparison.}.Proc Natl Acad Sci U S A. 85(8):2444-8.}
+     \keyword{datasets}

Added: pkg/man/mase.Rd
===================================================================
--- pkg/man/mase.Rd	                        (rev 0)
+++ pkg/man/mase.Rd	2010-08-25 12:44:39 UTC (rev 1749)
@@ -0,0 +1,10 @@
+\name{mase}
+     \docType{data}
+     \alias{mase}
+     \title{Example of results obtained after a call to read.alignment}
+     \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "mase" format.}
+     \usage{mase}
+     \format{A List of class alignment}
+     \source{http://www.clustal.org/}
+     \references{Faullcner.D.V. and Jurka,J. (1988) \emph{Multiple sequences alignment editor(MASE).} Trends Biochem. Sa., 13, 321-322.}
+     \keyword{datasets}

Added: pkg/man/msf.Rd
===================================================================
--- pkg/man/msf.Rd	                        (rev 0)
+++ pkg/man/msf.Rd	2010-08-25 12:44:39 UTC (rev 1749)
@@ -0,0 +1,9 @@
+\name{msf}
+     \docType{data}
+     \alias{msf}
+     \title{Example of results obtained after a call to read.alignment}
+     \description{This data set gives an example of a protein alignment obtained after a call to the function read.alignment on an alignment file in "msf" format.}
+     \usage{msf}
+     \format{A List of class alignment}
+     \source{http://www.ebi.ac.uk/2can/tutorials/formats.html#MSF/}
+     \keyword{datasets}

Added: pkg/man/phylip.Rd
===================================================================
--- pkg/man/phylip.Rd	                        (rev 0)
+++ pkg/man/phylip.Rd	2010-08-25 12:44:39 UTC (rev 1749)
@@ -0,0 +1,10 @@
+\name{phylip}
+     \docType{data}
+     \alias{phylip}
+     \title{Example of results obtained after a call to read.alignment}
+     \description{This data set gives an example of a amino acids alignment obtained after a call to the function read.alignment on an alignment file in "phylip" format.}
+     \usage{phylip}
+     \format{A List of class alignment}
+     \source{http://evolution.genetics.washington.edu/phylip.html}
+     \references{http://evolution.genetics.washington.edu/phylip.html}
+     \keyword{datasets}