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Tutorial: Phylo now supports NeXML; str(clade) is stable

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1 parent 978a3ae commit 203345d24801d0d59ed384f59d32c324a36ff9bc @etal etal committed Mar 14, 2013
Showing with 5 additions and 17 deletions.
  1. +5 −17 Doc/Tutorial.tex
@@ -9851,9 +9851,8 @@ \chapter{Phylogenetics with Bio.Phylo}
it aims to provide a common way to work with phylogenetic trees independently of the source data
format, as well as a consistent API for I/O operations.
-Bio.Phylo is described in an open-access BMC Bioinformatics article
-by Talevich et al.~(2012) \cite{talevich2012}, which you might also find
+Bio.Phylo is described in an open-access journal article \cite[Talevich
+\textit{et al.}, 2012]{talevich2012}, which you might also find helpful.
\section{Demo: What's in a Tree?}
@@ -10092,7 +10091,8 @@ \subsection{Coloring branches within a tree}
\section{I/O functions}
Like SeqIO and AlignIO, Phylo handles file input and output through four functions:
-\verb|parse|, \verb|read|, \verb|write| and \verb|convert|.
+\verb|parse|, \verb|read|, \verb|write| and \verb|convert|,
+all of which support the tree file formats Newick, NEXUS, phyloXML and NeXML.
The \verb|read| function parses a single tree in the given file and returns it. Careful; it
will raise an error if the file contains more than one tree, or no trees.
@@ -10130,7 +10130,7 @@ \section{I/O functions}
Convert files between any of the supported formats with the \verb|convert| function:
->>> Phylo.convert("tree1.xml", "phyloxml", "tree1.dnd", "newick")
+>>> Phylo.convert("tree1.dnd", "newick", "tree1.xml", "nexml")
>>> Phylo.convert("other_trees.xml", "phyloxml", "other_trees.nex", 'nexus")
@@ -10743,18 +10743,6 @@ \section{Future plans}
Bio.Phylo classes --- notably, calculating a consensus tree. If you find some functionality
lacking in Bio.Phylo, try poking throught Bio.Nexus to see if it's there instead.
- \item[NeXML support]
- Within the next few releases, we intend to add support for another file format, NeXML. This
- is unlikely to change the basic object hierarchy substantially, but could inspire some
- additions to the attributes of existing classes.
- \item[String representations]
- The string representations of some objects could change in future releases; we're
- still determining which ``informal'' representations are most useful most often. To
- future-proof your code against this, we recommend using the attributes of objects
- directly (e.g. \verb||) rather than automatic string conversion
- (\verb|str(my_clade)|) in scripts that require a consistent result.
We're open to any suggestions for improving the functionality and usability of this module;

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