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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

 (20)
library_books

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

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

[…] od 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. […]

call_split

Recombinant Viruses Initiated the Early HIV 1 Epidemic in Burkina Faso

2014
PLoS One
PMCID: 3960253
PMID: 24647246
DOI: 10.1371/journal.pone.0092423
call_split See protocol

[…] wo-parameter 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). […]

call_split

Effect of HIV 1 Subtypes on Disease Progression in Rural Uganda: A Prospective Clinical Cohort Study

2013
PLoS One
PMCID: 3741119
PMID: 23951241
DOI: 10.1371/journal.pone.0071768
call_split See protocol

[…] both the v3/v4 region of the env gene (approximately 400 bp) and a region of the gag gene encompassing most of both p17 and p24 (approximately 720 bp). Sequencing and phylogenetic analysis using the fastDNAml and Treecon package softwares was done as previously reported , . Samples from 83 incident cases enrolled between 2004 and 2010 were subtyped by sequencing and phylogenetic analysis in the p […]

library_books

Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source

2013
BMC Biol
PMCID: 3717074
PMID: 23870105
DOI: 10.1186/1741-7007-11-76

[…] nts were included or excluded in the outbreak depending on their grouping in the phylogenetic tree of the E1-E2 region sequences. The likelihood of each alternative topology was obtained with program fastDNAml [], allowing it to optimize branch lengths for each case. The LR for each patient was computed considering the whole data set: the PS, the controls, the excluded patients, the remaining pati […]

call_split

Factors Influencing the Diversity of Iron Uptake Systems in Aquatic Microorganisms

2012
Front Microbiol
PMCID: 3475125
PMID: 23087680
DOI: 10.3389/fmicb.2012.00362
call_split See protocol

[…] etrieved 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
Ecol Evol
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 in BEA […]

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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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