HAlign specifications

Information


Unique identifier OMICS_07879
Name HAlign
Alternative name HAlign-II
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

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Maintainer


  • person_outline Quan Zou <>

Information


Unique identifier OMICS_07879
Name HAlign
Alternative name HAlign-II
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages Java
Parallelization MapReduce
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Quan Zou <>

Publications for HAlign

HAlign in publications

 (4)
PMCID: 5751538
PMID: 29297337
DOI: 10.1186/s12918-017-0476-3

[…] handle the smallest dataset. so we only compare the performance with raxml, phangorn, stells and iq-tree []. all these three software tools need the aligned files as the input. so we firstly emloyed halign [] for multiple sequence alignment before the evolutionary trees reconstruction., the running time was compared and showed in fig. . the initial human mitochondrial genomes dataset is about 10  […]

PMCID: 5569537
PMID: 28852417
DOI: 10.1186/s13015-017-0113-0

[…] alignments are only possible for a small number of sequences of short length. therefore, heuristics and approximation methods have been applied in tools such as mafft [], clustal [], pasta [] and halign []. furthermore parallel computing has been introduced to reduce the actual running time for large scale alignments []. in our study, however, since we align only the three sequences […]

PMCID: 4961832
PMID: 27478823
DOI: 10.1155/2016/7604641

[…] combinatorial machine learning strategy that can improve prediction accuracy., machine learning techniques instead of traditional sequence alignment methods, such as psi-blast [], hmmer [], and halign [], are often used to identify special proteins. among these identification techniques, a support vector machine is the most common classifier used in computational proteomics, which involves […]

PMCID: 4914962
PMID: 27323846
DOI: 10.1038/srep28087

[…] the invariance. pssm matrix represents the comparison results between the input protein sequence and its homologous protein sequence in swiss-prot database. the multiple sequence alignment tools are halign and psi-blast (position-specific initiated blast). each input protein sequence generates a pssm matrix after multiple sequence alignment. the elements in pssm matrix characterize homology […]


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HAlign institution(s)
School of Computer Science and Technology, Tianjin University, Tianjin, China; Guangdong Province Key Laboratory of Popular High Performance Computers, Shenzhen University, Shenzhen, China

HAlign reviews

 (2)
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Quan Zou's avatar image No country

Quan Zou

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Desktop
The new URL is http://lab.malab.cn/soft/halign/index.html.

Web servers have been developed by the authors.
Anonymous user #1683's avatar image No country

Anonymous user #1683

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Desktop
A good tool on Hadoop platform