PFAAT pipeline

PFAAT specifications


Unique identifier OMICS_08907
Alternative 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 <>

Publications for Protein Family Alignment Annotation Tool

PFAAT IN pipelines

PMCID: 2890568
PMID: 20537180
DOI: 10.1186/1471-2164-11-369

[…] of the orthologs were collected in fasta format from the uniprot database. alignments were carried out using the l-ins-i method of the mafft software, version 6.713 [89] and evaluated using pfaat [90]. maximum likelihood trees were inferred using the treefinder software [91]. the whelan and goldman substitution model [92] was used., tgl, jg, and yw conceived and designed the study. […]

PMCID: 1325023
PMID: 16332259
DOI: 10.1186/1471-2164-6-173

[…] 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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