UNIX-style phylogenetic analyses on trees and sequences
phyx provides a convenient, lightweight and inclusive toolkit consisting of
programs spanning the wide breadth of programs utilized by researchers
performing phylogenomic analyses. Modeled after Unix/GNU/Linux command
line tools, individual programs perform a single task and operate on
standard I/O streams. A result of this stream-centric approach is that, for
most programs, only a single sequence or tree is in memory at any moment.
Thus, large datasets can be processed with minimal memory requirements.
phyx’s ever-growing complement of programs consists of over 35 programs
focused on exploring, manipulating, analyzing and simulating phylogenetic
objects (alignments, trees and MCMC logs). As with standard Unix command
line tools, these programs can be piped (together with non-phyx tools),
allowing the easy construction of efficient analytical pipelines.
