LALIGN pipeline

LALIGN specifications

Information


Unique identifier OMICS_15830
Name LALIGN
Interface Web user interface
Restrictions to use None
Input data A query sequence
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

LALIGN IN pipelines

 (6)
2014
PMCID: 4160248
PMID: 25207969
DOI: 10.1371/journal.pone.0107311

[…] cmb-ra against the deduced amino acid sequences of dipteran orthologs was performed using t-coffee (v6.85) [56], [57] using the following pair-wise alignment methods: the 10 best local alignments (lalign_pair), an accurate global alignment (slow_pair) [56], [57]. this alignment was used to construct a maximum likelihood tree using the phyml program (v3.0 alrt) [58] using the wag substitution […]

2014
PMCID: 4327750
PMID: 28324357
DOI: 10.1007/s13205-014-0195-z

[…] to protein sequences. phylogenetic relationships among the identified sequences were calculated using phylip (felsenstein 1989). sequence identity matrix of all the thirteen ppos was computed using lalign program (http://workbench.sdsc.edu/). the molecular weight (statistical analysis of protein sequence (saps), brendel et al. 1992) and isoelectric point (http://seqtool.sdsc.edu/cgi/bw.cgi) […]

2013
PMCID: 3689728
PMID: 23805309
DOI: 10.1371/journal.pone.0067327

[…] other efforts were made to minimise suffering., blast searches were performed via the ncbi website (http://blast.ncbi.nlm.nih.gov/blast.cgi). pairwise alignments were made using william pearson’s lalign software available at http://www.ch.embnet.org/software/lalign_form.html or using vectornti alignx software (invitrogen). cyclin (cd00043 (cyclin superfamily) and/or cog5024 (cyclin-like […]

2013
PMCID: 3689728
PMID: 23805309
DOI: 10.1371/journal.pone.0067327

[…] were performed via the ncbi website (http://blast.ncbi.nlm.nih.gov/blast.cgi). pairwise alignments were made using william pearson’s lalign software available at http://www.ch.embnet.org/software/lalign_form.html or using vectornti alignx software (invitrogen). cyclin (cd00043 (cyclin superfamily) and/or cog5024 (cyclin-like superfamily ccl1 (tigr00569)) and kinase (pkc_like superfamily) […]

2011
PMCID: 3224142
PMID: 21867507
DOI: 10.1186/1471-2229-11-119

[…] tree was constructed using the phylogeny platform http://www.phylogeny.fr/[54] and comprised the following steps. sequences were aligned using t-coffee (v6.85) using the 10 best local alignments (lalign_pair), an accurate global alignment (slow_pair). after alignment, ambiguous regions were removed with gblocks (v0.91b). minimum length of a block after gap cleaning was set at 10; no gap […]

LALIGN institution(s)
Department of Computer Science, Michigan Technological University, Houghton, MI, USA; Department of Computer Science, The Pennsylvania State University, University Park, PA, USA
LALIGN funding source(s)
This work was supported by Grant R01 LM05110 form the National Library of Medicine.

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