POY 4.1.2 released

[Andres Varon]

Hello Everyone,

I am pleased to announce the release of POY version 4.1.2, available at

http://research.amnh.org/scicomp/projects/poy.php

This update has a number of important bugs fixed, as well as new features. The complete list of changes is below. Among these changes, I would highlight the vastly improved NEXUS support (e.g. POY can now output NEXUS files), and the experimental addition of double cut and join to calculate rearrangement distance in chromosomal characters. Bugs fixed affected the diagnosis, search speed, constraints, and support value calculations.

I hope you will find this version better, and enjoy using POY to explore, analyze, and publish your data. Special thanks to those of you have given us some great feedback in the past months. Every comment help us making a better application.

best,

Andres Varon

New Features:

    - Added read (prealigned:(....., gap_opening:INT)) to read

      prealigned sequences and assign each indel block a gap opening

      cost.

    - The build process now uses ocamlbuild instead of plain

      Makefiles.

    - The distributed binaries are the first to support plugins for

      POY, but the feature is still experimental.

    - Improved the NEXUS file format support, by adding the POY block,

      which now includes: GAPOPENING, TCM, and WTSET. All the

      characters in POY can now be stored in one NEXUS file that can

      be reloaded later. The support for NEXUS files has improved to

      allow more transparent interaction with other applications.

    - POY now interprets all the ASSUMPTION block commands in NEXUS

      files that the program can apply (e.g. EXSET, TYPESET, and

      USERTYPE).

    - Added report (nexus) and report (trees:(nexus)) to generate

      output in nexus format.

    - report ("out.ext", data, trees) produce NEXUS or hennig format

      depending on ext. If the extension of the filename to which data

      and trees are generated is "nexus" or "nex" then the data and

      trees are generated in NEXUS format. If the extension is "hen",

      "hennig", or "ss", then the format is Hennig86. For example,

      report ("out.nexus", data, trees) is equivalent to report

      ("out.nexus", nexus, trees:(nexus)).

    - Replace spaces with underscores in taxon names of NEXUS files.

    - Added support to newick files with branch lengths. The branches

      are ignored.

    - Added support to 1~4 ranges.

    - Bremer support values can output on the branches of a consensus

      tree or any user provided input tree. (See the new commands

      below.)

    - Added build (nj) to build a tree using the neighbor joining

      algorithm. The algorithm implementation is deterministic, so

      only one tree can be produce for each dataset.

New Commands:

    - report (nexus trees:(nexus)).

    - transform (dynamic_pam:(locus:dcj:INT))

    - report (supports:bremer:of_file:("file1", "file2", ...))

Features eliminated:

    - Dropped ti and td

    - ':' is not accepted in a taxon name. This constraint is required for the 

      newick file format. For example "mytaxon:1" is not an acceptable 

      taxon name anymore.

Bugs Fixed:

    - Fixed issue 72.

    - Fixed incorrect description of select (missing) in the

      documentation.

    - Annotated chromosomes could produce incorrect costs

    - Fixed compilation problems of the portal

    - Data.get_tcm2d error (Buz Wilson, Katrina Menard).

    - Sankoff characters where not applied the user defined weight.

    - Branch collapsing in Sankoff and Additive characters could be

      incorrect.

    - Tree scores with additive characters may be incorrect (Taran

      Grant). This only happened if the additive character had state

      7.

    - search (constraint) and swap (constraint) have multiple fixes to

      better guarantee the restrictions set by the constraint.

    - 0 length branches now appear with 0 bremer support when bremer is

      reported.

    - Fixed compilation error in Mac OS X 64 bits using OCaml 3.11.0.

    - The total rearrangement cost included indels for rearranged

      elements.