POY version 5: phylogenetic analysis using dynamic homologies under multiple optimality criteria.

We present POY version 5, an open source program for the phylogenetic analysis of diverse data types including qualitative, aligned sequences, unaligned sequences, genomic data, and user-defined sequences. In addition to the maximum-parsimony optimality criterion supported by POY4, POY5 supports several types of maximum likelihood as well as posterior probability. To make these analyses feasible, new heuristic search algorithms and parallelization options have been implemented for all criteria.

Local search for the generalized tree alignment problem.

Background: A phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide.

The tree alignment problem.

Background: The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequence alignments, and among these, the minimization of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization as the Tree Alignment Problem.

The Supramap project: linking pathogen genomes with geography to fight emergent infectious diseases.

Novel pathogens have the potential to become critical issues of national security, public health and economic welfare. As demonstrated by the response to Severe Acute Respiratory Syndrome (SARS) and influenza, genomic sequencing has become an important method for diagnosing agents of infectious disease. Despite the value of genomic sequences in characterizing novel pathogens, raw data on their own do not provide the information needed by public health officials and researchers.

POY version 4: phylogenetic analysis using dynamic homologies.

We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data. POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance). Compared with previous versions, POY 4 provides greater flexibility, a larger number of supported parameter sets, numerous execution time improvements, a vastly improved user interface, greater quality control, and extensive documentation.

Pairwise alignment with rearrangements.

The increase of available genomes poses new optimization problems in genome comparisons. A genome can be considered as a sequence of characters (loci) which are genes or segments of nucleotides. Genomes are subject to both nucleotide transformation and character order rearrangement processes.