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May 31, 2011, 5:01:41 PM5/31/11

to DendroPy Announcements

DendroPy 3.8.0 has been released.

This release is include some major extensions/`changes to both the

core DendroPy library as well as the bundled SumTrees application. In

addition, the tutorial has been extended to cover some tree

manipulation opertions (rooting, rotating, and pruning) in detail.

SumTrees now has greatly expanded abilities to deal with ultrametric

trees, as

well as summarizing edge length and tree probability information:

- SumTrees can now summarize edge lengths on target trees in

different

ways:

- `-e mean-length`: sets the edge lengths of the target/

consensus

tree(s) to the mean of the lengths of the corresponding

edges of the

input trees.

- `-e median-length`: sets the edge lengths of the target/

consensus

tree(s) to the median of the lengths of the corresponding

edges of

the input trees.

- `-e median-age`: adjusts the edge lengths of the target/

consensus

tree(s) such that the node ages correspond to the median age

of

corresponding nodes of the input trees [requires rooted

ultrametric

trees].

- `-e mean-age`: adjusts the edge lengths of the target/

consensus

tree(s) such that the node ages correspond to the mean age

of

corresponding nodes of the input trees [requires rooted

ultrametric

trees].

- SumTrees will now annotate edges with summaries (mean, median,

standard

deviation, range, 95% highest posterior density, 5% and 95%

quantiles,

etc.) of the distribution of edge lengths across across input

trees.

- SumTrees will now annotate nodes with summaries (mean, median,

standard

deviation, range, 95% highest posterior density, 5% and 95%

quantiles,

etc.) of the distribution of ages across across input trees if

the trees

are indicated to be ultrametric with the "``--ultrametric``"

flag

[requires rooted ultrametric trees].

- SumTrees will now be interpret and handle tree weights if the

`--weighted-trees` option is specified.

- SumTrees will now report topology frequencies/probabilities, if

given the

`--trprobs` option.

- SumTrees can now handle arbitrarily-large numbers of files.

- SumTrees creates a rooted consensus tree if input trees are

specified to

be rooted using the `--rooted-trees` flag (or rooted trees are

assumed as

with the '--ultrametric' flag).

- More information as well as detailed user guide available here:

http://packages.python.org/DendroPy/scripts/sumtrees.html

The core DendroPy library as well has many new features and

enhancements, including:

- Tree objects can now be rerooted at midpoint (see

`Tree.reroot_at_midpoint()`).

- Annotations (i.e., attributes of Tree, Node or Edge objects that

have had "annotate()" called on them) can now be written as metadata

comments ("[&field=value]") when writing NEXUS/NEWICK format if the

keyword argument `annotations_as_comments` is used.

- When reading in NEXUS/NEWICK format trees, specifying

`extract_comment_metadata=True` will result in metadata comments being

pulled into dictionary, with keys being fieldnames and values being

the field values.

- When reading NEXUS format data, SETS blocks will be processed,

and character sets parsed into the relevant CharacterDataMatrix.

- Character sets (as, for example, parsed out of NEXUS SETS

blocks: see above) can be exported as new CharacterDataMatrix objects,

and be saved/manipulated/etc. independentally.

- When writing in NEXUS or NEWICK formats, the

`write_item_comments` keyword argument (`True` or `False`) can control

whether extended comments associated with nodes on trees will be

written or not.

- TopologyCounter class added to dendropy.treesum: allows for

tracking of topology frequencies.

- `treesplits.tree_from_splits()` allows constructing of (topology-

only) trees from a set of splits.

- Most functionality that used to be 'dendropy.treemanip' has now

been migrated as native methods of the dendropy.Tree class.

'dendropy.treemanip' will be deprecated.

- Trees can now be pruned based on a list of taxa labels to remove

or keep (previously, the methods would only accept lists of Taxon

objects).

- A detailed change log can be found here:

http://packages.python.org/DendroPy/changes.html

The latest release is available from:

http://pypi.python.org/pypi/DendroPy

This release is include some major extensions/`changes to both the

core DendroPy library as well as the bundled SumTrees application. In

addition, the tutorial has been extended to cover some tree

manipulation opertions (rooting, rotating, and pruning) in detail.

SumTrees now has greatly expanded abilities to deal with ultrametric

trees, as

well as summarizing edge length and tree probability information:

- SumTrees can now summarize edge lengths on target trees in

different

ways:

- `-e mean-length`: sets the edge lengths of the target/

consensus

tree(s) to the mean of the lengths of the corresponding

edges of the

input trees.

- `-e median-length`: sets the edge lengths of the target/

consensus

tree(s) to the median of the lengths of the corresponding

edges of

the input trees.

- `-e median-age`: adjusts the edge lengths of the target/

consensus

tree(s) such that the node ages correspond to the median age

of

corresponding nodes of the input trees [requires rooted

ultrametric

trees].

- `-e mean-age`: adjusts the edge lengths of the target/

consensus

tree(s) such that the node ages correspond to the mean age

of

corresponding nodes of the input trees [requires rooted

ultrametric

trees].

- SumTrees will now annotate edges with summaries (mean, median,

standard

deviation, range, 95% highest posterior density, 5% and 95%

quantiles,

etc.) of the distribution of edge lengths across across input

trees.

- SumTrees will now annotate nodes with summaries (mean, median,

standard

deviation, range, 95% highest posterior density, 5% and 95%

quantiles,

etc.) of the distribution of ages across across input trees if

the trees

are indicated to be ultrametric with the "``--ultrametric``"

flag

[requires rooted ultrametric trees].

- SumTrees will now be interpret and handle tree weights if the

`--weighted-trees` option is specified.

- SumTrees will now report topology frequencies/probabilities, if

given the

`--trprobs` option.

- SumTrees can now handle arbitrarily-large numbers of files.

- SumTrees creates a rooted consensus tree if input trees are

specified to

be rooted using the `--rooted-trees` flag (or rooted trees are

assumed as

with the '--ultrametric' flag).

- More information as well as detailed user guide available here:

http://packages.python.org/DendroPy/scripts/sumtrees.html

The core DendroPy library as well has many new features and

enhancements, including:

- Tree objects can now be rerooted at midpoint (see

`Tree.reroot_at_midpoint()`).

- Annotations (i.e., attributes of Tree, Node or Edge objects that

have had "annotate()" called on them) can now be written as metadata

comments ("[&field=value]") when writing NEXUS/NEWICK format if the

keyword argument `annotations_as_comments` is used.

- When reading in NEXUS/NEWICK format trees, specifying

`extract_comment_metadata=True` will result in metadata comments being

pulled into dictionary, with keys being fieldnames and values being

the field values.

- When reading NEXUS format data, SETS blocks will be processed,

and character sets parsed into the relevant CharacterDataMatrix.

- Character sets (as, for example, parsed out of NEXUS SETS

blocks: see above) can be exported as new CharacterDataMatrix objects,

and be saved/manipulated/etc. independentally.

- When writing in NEXUS or NEWICK formats, the

`write_item_comments` keyword argument (`True` or `False`) can control

whether extended comments associated with nodes on trees will be

written or not.

- TopologyCounter class added to dendropy.treesum: allows for

tracking of topology frequencies.

- `treesplits.tree_from_splits()` allows constructing of (topology-

only) trees from a set of splits.

- Most functionality that used to be 'dendropy.treemanip' has now

been migrated as native methods of the dendropy.Tree class.

'dendropy.treemanip' will be deprecated.

- Trees can now be pruned based on a list of taxa labels to remove

or keep (previously, the methods would only accept lists of Taxon

objects).

- A detailed change log can be found here:

http://packages.python.org/DendroPy/changes.html

The latest release is available from:

http://pypi.python.org/pypi/DendroPy

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