Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
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4,722 citations
Cites methods from "Fast, scalable generation of high‐q..."
...Hence, we replaced the programs BLAST and ClustalW2 by their latest revisions (BLAST+ (17) and Clustal Omega (18), respectively) to gain in scalability, accuracy and performance....
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4,135 citations
Cites background or methods from "Fast, scalable generation of high‐q..."
...[4], for some MAFFT options available on our online server...
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...However, there are also other popular programs, such as Clustal Omega [4] and UPP [22], for this purpose....
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...Clustal Omega uses the mBed algorithm [23] to build a guide tree with a time complexity of OðN log NÞ....
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3,527 citations
Cites methods from "Fast, scalable generation of high‐q..."
...Protein sequence alignments were done using Clustal Omega (33)....
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3,319 citations
References
37,524 citations
"Fast, scalable generation of high‐q..." refers methods in this paper
...Code for fast UPGMA and guide tree handling routines was adopted from MUSCLE (Edgar, 2004)....
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...Here, we present results from a range of packages tested on three benchmarks: BAliBASE (Thompson et al, 2005), Prefab (Edgar, 2004) and an extended version of HomFam (Blackshields et al, 2010)....
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...For these tests, we just report results using the default settings for all programs but with two exceptions, which were needed to allow MUSCLE (Edgar, 2004) and MAFFT to align the biggest test cases in HomFam....
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...For these tests, we just report results using the default settings for all programs but with two exceptions, which were needed to allow MUSCLE (Edgar, 2004) and MAFFT to align the biggest test cases in HomFam....
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25,325 citations
14,075 citations
"Fast, scalable generation of high‐q..." refers background in this paper
...There are already widely available collections of HMMs from many sources such as Pfam...
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12,003 citations
"Fast, scalable generation of high‐q..." refers background in this paper
...1 (http://www.clustal.org) DIALIGN 2.2.1 (http://dialign.gobics.de/) FSA 1.15.5 (http://sourceforge.net/projects/fsa/) Kalign 2.04 (http://msa.sbc.su.se/cgi-bin/msa.cgi) MAFFT 6.857 (http://mafft.cbrc.jp/alignment/software/source.html) MSAProbs 0.9.4 (http://sourceforge.net/projects/msaprobs/files/) MUSCLE version 3.8.31 posted 1 May 2010 (http://www.drive5. com/muscle/downloads.htm) PRANKv.100802, 2August 2010 (http://www.ebi.ac.uk/goldman-srv/ prank/src/prank/) Probalign v1....
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...The consistency-based programsMSAprobs,MAFFT L-INS-i, Probalign, Probcons and T-Coffee, are again the most accurate but with long run times....
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...For these tests, we just report results using the default settings for all programs but with two exceptions, which were needed to allow MUSCLE (Edgar, 2004) and MAFFT to align the biggest test cases in HomFam....
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...There is then a gap to the faster progressive based programs of MUSCLE, MAFFT, Kalign (Lassmann and Sonnhammer, 2005) and Clustal W. Results from testing large alignments with up to 50000 sequences are given in Table III using HomFam....
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...MAFFT with default settings, has a limit of 20000 sequences and we only use MAFFT with –parttree for the last section of Table III....
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9,415 citations