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seqmagick specifications

Desktop

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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Issues: https://github.com/fhcrc/seqmagick/issues

seqmagick citations

(2)

Non Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections

2015

PLoS Pathog

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 […]

Rapid draft sequencing and real time nanopore sequencing in a hospital outbreak of Salmonella

2015

Genome Biol

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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