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DendroPy Phylogenetic Computing Library — DendroPy 4.3.0 documentation

DendroPy 4.3.0 documentation. DendroPy Phylogenetic Computing Library. DendroPy is a Python. DendroPy is a pure-Python library with no dependencies, and runs under any version of Python 3 and Python 2.7. If you want to run DendroPy under Python version of less than 2.7, you should download the DendroPy legacy release. Changed in version 4.0.0:. Python 2.4, 2.5, and 2.6 support removed. Python 3.x support added. DendroPy is fully easy-installable and can be installed using pip. Sudo pip install -U dendropy.

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DendroPy Phylogenetic Computing Library — DendroPy 4.3.0 documentation | dendropy.org Reviews

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DendroPy 4.3.0 documentation. DendroPy Phylogenetic Computing Library. DendroPy is a Python. DendroPy is a pure-Python library with no dependencies, and runs under any version of Python 3 and Python 2.7. If you want to run DendroPy under Python version of less than 2.7, you should download the DendroPy legacy release. Changed in version 4.0.0:. Python 2.4, 2.5, and 2.6 support removed. Python 3.x support added. DendroPy is fully easy-installable and can be installed using pip. Sudo pip install -U dendropy.

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DendroPy Phylogenetic Computing Library — DendroPy 4.3.0 documentation | dendropy.org Reviews

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DendroPy 4.3.0 documentation. DendroPy Phylogenetic Computing Library. DendroPy is a Python. DendroPy is a pure-Python library with no dependencies, and runs under any version of Python 3 and Python 2.7. If you want to run DendroPy under Python version of less than 2.7, you should download the DendroPy legacy release. Changed in version 4.0.0:. Python 2.4, 2.5, and 2.6 support removed. Python 3.x support added. DendroPy is fully easy-installable and can be installed using pip. Sudo pip install -U dendropy.

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dendropy.org

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Index — DendroPy 4.2.0 documentation

http://www.dendropy.org/genindex.html

DendroPy 4.2.0 documentation. Add () (dendropy.datamodel.treecollectionmodel.TreeArray method). Dendropy.datamodel.treecollectionmodel.TreeList method). Contains () (dendropy.datamodel.charmatrixmodel.CharacterMatrix method). Dendropy.datamodel.taxonmodel.TaxonNamespace method). Copy () (dendropy.datamodel.basemodel.Annotable method). Delattr (dendropy.datamodel.basemodel.Annotable attribute). Dendropy.datamodel.basemodel.Annotation attribute). Dendropy.datamodel.treemodel.Edge attribute). Delattr () (de...

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Glossary and Terminological Reference — DendroPy 4.2.0 documentation

http://www.dendropy.org/glossary.html

DendroPy 4.2.0 documentation. Glossary and Terminological Reference. The full set of nodes. From which a given node. Has descended (i.e., the given node’s parent, parent’s parent, parent’s parent’s parent, and so on until the root. Or the seed node. Of the tree, inclusive). That is ancestral with respect to another node. Leaf or tip nodes. Can never be basal, except if the tree consists of only a single node (i.e., the seed node. Is a leaf node. The basal-most node of a tree is the seed or root node.

3

DendroPy 4 Changes and Migration Primer — DendroPy 4.2.0 documentation

http://www.dendropy.org/migration.html

DendroPy 4.2.0 documentation. DendroPy 4 Changes and Migration Primer. Updated for full (and exclusive) Python 3.x compatibility. Faster, better, stronger! Core serialization/deserialization infrastructure rewritten from the ground up, with. Optimizations for speed and reliability. Compatibility: Python 3 is fully supported. The only version of Python 2 supported is Python 2.7. Python 2: Python 2.7. Python 3: Python 3.1, 3.2, 3.3, 3.4. For calculation of statistics, metrics, and values on a single tree.

4

PHYLIP — DendroPy 4.2.0 documentation

http://www.dendropy.org/schemas/phylip.html

DendroPy 4.2.0 documentation. DendroPy Schemas: Phylogenetic and Evolutionary Biology Data Formats. 8211; When reading into a. Object, the type of data must be specified: “dna”, “rna”, “protein”, “restriction”, “infinite”, “standard”, or “continuous”. Object to be used to manage the alphabet of the characters (. Then data is given in ‘strict’ format, where first 10 characters are the taxon label and remaining characters are the sequence. Default is. Or two or more (if. Underscores are not converted.

5

Programs and Applications — DendroPy 4.2.0 documentation

http://www.dendropy.org/programs/index.html

DendroPy 4.2.0 documentation. SumTrees: Phylogenetic Tree Summarization and Annotation. Where to Find the Package. How to Install the Package. How to Use the Program. Summarization of Posterior Probabilities of Clades with a Consensus Tree. Summarization of Posterior Probabilities of Clades with a Maximum Clade Credibility Tree (MCCT). Non-parametric Bootstrap Support of a Model Tree. Set Node Ages of Target or Summary Tree(s) to Mean/Median Node Age of Input Trees. Running in Parallel Mode. Join the Den...

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