PAGAN2

PAGAN2 is a general-purpose method for the alignment of DNA, codon and amino-acid sequences as graphs. It aligns sequences either with pileup or, when related by a tree, using phylogeny-aware progressive alignment algorithm. In both cases it uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. PAGAN2 is largely compatible with PAGAN but implements new algorithms for alignment anchoring and memory handling. As a result, PAGAN2 can align sequences of several hundreds of kilobases in length.

homepage: https://github.com/ariloytynoja/pagan2-msa

version	versionsuffix	toolchain
1.53_20230824	-linux64	system

(quick links: (all) - 0 - a - b - c - d - e - f - g - h - i - j - k - l - m - n - o - p - q - r - s - t - u - v - w - x - y - z)