Hal protocols

View Hal computational protocol

Hal statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Bioinformatics workflows chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Hal specifications

Information


Unique identifier OMICS_17820
Name Hal
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Alpha
Requirements
BioPerl formatdb, BLASTALL, Gblocks, ProtTest
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Barbara Robbertse <>

Publication for Hal

Hal in pipelines

 (6)
2016
PMCID: 4907049
PMID: 27296936
DOI: 10.1186/s12864-016-2738-7

[…] best blastp-hits method was used to identify orthologs in each genome []. these were clustered with the mcl algorithm and aligned with muscle [, ]. mcl inflation parameters were used as in the hal paper ([]; there were 13 inflation parameters), groups were selected starting from the highest moving to the lowest inflation parameter, selecting groups containg bidirectional best hits […]

2015
PMCID: 4494064
PMID: 25977457
DOI: 10.1093/gbe/evv090

[…] online). assembly statistics are summarized in supplementary table s2, supplementary material online., orthologous clusters were identified across the 40 different genomes using the pipeline hal (). briefly, orthologous clusters were identified across a range of inflation parameters (1.2, 3.0, 5.0) using the markov cluster algorithm. these clusters were then filtered using custom perl […]

2015
PMCID: 4658809
PMID: 26607873
DOI: 10.1186/s12864-015-2229-2

[…] of orthologous protein clusters [http://sourceforge.net/projects/bio-hal/]. orthologous protein clusters [] were identified by using blastp and markov cluster algorithm (mcl) tool [] integrated in hal pipeline. only non-redundant clusters that consisted of protein sequences with best hits to proteins from own cluster were filtered out. protein sequences for these orthologous clusters […]

2015
PMCID: 4663792
PMID: 26617401
DOI: 10.1038/srep17394

[…] with raxml 8.0.22 (100 bootstrap replications). the proteomes of four fabaceae species and a. thaliana were aligned, and single gene clusters filtered and concatenated after removing gaps using hal. a phylogenetic tree based on these data was built with mega6 using maximum-likelihood and 100 bootstrap replications. divergence times in the phylogenetic tree were calculated with the reltime […]

2013
PMCID: 3538342
PMID: 23316438
DOI: 10.1534/g3.112.004044

[…] genetic flexibility and its role in pathogenicity as well as the identification of pathogen-specific genes will be discussed., phylogenetic analyses were performed using the phylogenetic pipeline, hal (, ). to summarize in brief, orthologous clusters of proteins were estimated from 16 ascomycota genomes using the program mcl () across 13 inflation parameters (1.1, 1.2, 1.3, 1.4, 1.5, 1.7, 2.0, […]


To access a full list of citations, you will need to upgrade to our premium service.

Hal in publications

 (19)
PMCID: 5819190
PMID: 29463214
DOI: 10.1186/s12864-018-4549-5

[…] 1, we inferred a phylogenetic tree to evaluate the evolutionary relationships between the selected species. a super alignment of the selected fungal proteomes was constructed with the hal pipeline [], allowing for no missing data. poorly aligned positions and ones with gaps were removed with gblocks 0.91b []. the following stringent parameters were used: the maximum number […]

PMCID: 5395668
PMID: 28420738
DOI: 10.1128/mBio.00413-17

[…] aaa240-o15, and chloroflexi bacterium scgc ab-629-p13. pirellula staleyi dsm 6068 was used as the outgroup. phylogenomic trees and orthology were determined with a modern reimplementation of the hal pipeline workflow (, ) described previously by brown et al. ()., genome size estimates were obtained using a set of 71 single-copy conserved core genes derived through a combinatorial core genome […]

PMCID: 5037894
PMID: 27671367
DOI: 10.1186/s12864-016-3083-6

[…] with raxml 8.0.22 [] (100 bootstrap replications). the proteomes of six fabaceae species and a. thaliana were aligned, and single gene clusters filtered and concatenated after removing gaps using hal []. a phylogenetic tree based on these data was built with mega6 [] using maximum-likelihood and 100 bootstrap replications., the perl script misa (microsatellite; […]

PMCID: 5023957
PMID: 27601008
DOI: 10.1038/ncomms12662

[…] of lifestyles (biotrophic/hemibiotrophic/necrotrophic pathogens, white rot/brown rot/litter/aquatic saprotrophs and ericoid/ecm species). genome-scale phylogenetic analyses were conducted with the hal pipeline. briefly, orthologous clusters (oc) were identified using mcl across inflation parameters 1, 2, 3 and 5. ocs were filtered to retain non-redundant, single-copy clusters (one protein per […]

PMCID: 4921968
PMID: 27345283
DOI: 10.1038/srep28598

[…] hormone function (http://ahd.cbi.pku.edu.cn/) and kegg annotation (http://www.genome. jp/tools/kaas/)., the phylogenetic tree was constructed following the hal analysis. briefly, the orthomcl v1.4 was applied to identify candidate orthologs from 20 selected plant genomes and e. aureum gene set. the all-vs-all blastp implemented in orthomcl was executed […]


To access a full list of publications, you will need to upgrade to our premium service.

Hal institution(s)
National Center for Biotechnology Information, Bethesda, MD, USA; Peace Corps; Oregon State University, Corvallis, OR, USA
Hal funding source(s)
Supported by a National Science Foundation grant (DEB-0732993).

Hal reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Hal