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)Non Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections
[…] 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
[…] 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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