seqmagick specifications

Information


Unique identifier OMICS_11290
Name seqmagick
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTA
Output format PHYLIP, FASTA
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
BioPython
Maintained Yes

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seqmagick in publications

 (2)
PMCID: 4646697
PMID: 26571270
DOI: 10.1371/journal.ppat.1005225

[…] and frameshift mutation characters, as identified by macse, were replaced with ambiguous "n" characters, putting the corresponding sequences in frame. the resulting sequences were translated using seqmagick v0.6.0 [], and aligned using mafft v7.058b [] resulting in amino acid alignments that were used by seqmagick backtrans-align to produce a backtranslation alignment., phylogenetic trees […]

PMCID: 4702336
PMID: 26025440
DOI: 10.1186/s13059-015-0677-2

[…] and regions of putative recombination. variant alleles for each sample were concatenated into a fasta file using vcf2phyloviz.py []. this file was de-duplicated using the mogrify command in seqmagick (version 0.6.0) to remove identical sequences which can affect placements. a phylogenetic reconstruction was created using fasttree (version 2.1.7) following a generalised time reversible […]


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seqmagick institution(s)
The Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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