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fastDNAml specifications

Information


Unique identifier OMICS_15837
Name fastDNAml
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Pascal
Computer skills Advanced
Version 1.2.2
Stability Stable
Source code URL http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml_1.2.2-macos9.sit
Maintained Yes

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Publication for fastDNAml

fastDNAml citations

 (19)
library_books

Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes

2014
PMCID: 4135293
PMID: 25187685
DOI: 10.6026/97320630010443

[…] as well. as most of our sequences belong to distantly related sequences and only seven sequences were in our data set so it was computationally inexpensive to perform maximum likelihood method fastdnaml tool. same dataset was also verified through bioedit software by applying neighbor-joining/upgma method., archea: prokaryote: eukaryote.gb files with nucleotide and protein sequences […]

library_books

Recombinant Viruses Initiated the Early HIV 1 Epidemic in Burkina Faso

2014
PMCID: 3960253
PMID: 24647246
DOI: 10.1371/journal.pone.0092423

[…] model included in the phylip package (version 3.5c) with and without bootstrapping. sivcpz sequences were used as outgroups. it was further verified with maximum likelihood method using fastdnaml program (http://www.genestudio.com)., subtype and crf designations were determined from phylogenetic analysis, and sequences were input into the mega program, version 2.0 to calculate […]

library_books

Factors Influencing the Diversity of Iron Uptake Systems in Aquatic Microorganisms

2012
PMCID: 3475125
PMID: 23087680
DOI: 10.3389/fmicb.2012.00362

[…] from genbank along with the e. coli 16s rrna sequence. these were aligned using muscle and imported into the arb software (ludwig et al., ). a maximum likelihood tree was calculated with the fastdnaml (olsen et al., ) implementation in arb using a filter for base 800 to base 1300 encompassing and extending on both sides, the v6 hypervariable region in e. coli. an in-house script was used […]

library_books

Locus specific view of flax domestication history

2012
PMCID: 3297184
PMID: 22408732
DOI: 10.1002/ece3.57

[…] of 46 nucleotides occurred at position 562 of the alignment, which was used as a character in building the network. the phylogenetic topology of the network was confirmed through maximum likelihood (fastdnaml; ), neighbor-joining analyses (neighbor; ), and neighbornet (splitstree; )., the date estimates for nodes from the network were corroborated using the bayesian mcmc approach implemented […]

library_books

Biodiversity of Archaea and floral of two inland saltern ecosystems in the Alto Vinalopó Valley, Spain

2010
PMCID: 2984398
PMID: 20942947
DOI: 10.1186/1746-1448-6-10

[…] from genbank http://www.ncbi.nlm.nih.gov using blastn and blastp. alignments of the 16s rrna sequences were created using clustalw., tree topologies were evaluated using the maximum likelihood (fastdnaml) method., a volume of 0.5 ml from each sample was used to assess the presence of dunaliella and artemia by optical microscopy with an axiostar zeiss microscope or a magnifying glass, […]

library_books

Genetic Signatures in the Envelope Glycoproteins of HIV 1 that Associate with Broadly Neutralizing Antibodies

2010
PMCID: 2951345
PMID: 20949103
DOI: 10.1371/journal.pcbi.1000955

[…] reducing the impact of inter-subtype recombination on the analyses. we implement are ancestral reconstruction through maximum likelihood phylogenies, using code originally based on gary olsen's fastdnaml , with a gtr model with a likelihood estimate of rate variation per site, and adapted to given ancestral states at all nodes ., while a maximum likelihood tree framework enables us to model […]


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fastDNAml institution(s)
Department of Microbiology, University of Illinois, Urbana, IL, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
fastDNAml funding source(s)
This work was supported in part by the Applied Mathematical Sciences subprogram of the Office of Energy Research, US Department of Energy, under Contract W-31-109-Eng-38 and by National Science Foundation grant DIR 89-17863 is the recipient of a National Science Foundation Presidential Young Investigator Award.

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