PyCogent Free and open source Python sequence toolkit
Download

PyCogent Ranking & Summary

PyCogent Tags

toolkit python toolkit sequence toolkit python sequence sequence PyCogent

PyCogent Description

Free and open source Python sequence toolkit PyCogent is a toolkit for making sense from sequence. PyCogent includes connectors to remote databases, controllers for 3rd party applications and built-in generalized probabilistic techniques for working with biological sequences. Requirements: · Python 2.5.1 or later · NumPy 1.0 or later What's New in This Release: · PyPi install now works, see work around on bug 2807542, 2807539 Cogent 1.2 - 1.3 New Features · Python2.6 is now supported · added cogent.cluster.nmds, code to perform nonmetric multidimensional scaling. Not as fast as others (e.g.: R, MASS package, isoMDS) · Documentation ported to using the Sphinx documentation generator. · Major additions to documentation in doc/examples. · Added partial support for querying the Ensembl MySQL databases. This capacity has additional dependencies (MySQL-python and SQLAlchemy). This module should be considered alpha level code, (although it has worked reliably for some time in the hands of the developers). · Introduced a new substitution model family. This family has the same form as that originally described by Muse and Gaut.

PyCogent Related Software