PFAAT specifications


Unique identifier OMICS_08907
Name Protein Family Alignment Annotation Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes


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  • person_outline Daniel R Caffrey <>

PFAAT articles

PFAAT citation

PMCID: 1325023

[…] to ensure integrity of transmembrane domains and proper alignment of anchoring or motifs. n- and c-terminal tails were trimmed for all alignments. the neighbor-joining algorithm as implemented by pfaat was used to generate unrooted phylogenetic trees from these alignments using the blosum 50 similarity matrix; positions with greater than 40% gaps were excluded. one thousand bootstraps […]

PFAAT institution(s)
Pfizer Discovery Technology Center, Cambridge, MA, USA; Neogenesis Drug Discovery, Cambridge, MA, USA

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