Sequence Manipulation and Viewing
Sequence Manipulation and Viewing
Mesquite (GUI)
Aliview (GUI)
Geneious (GUI)
BioPython
DendroPy
PyCogent
Site Striping and Masking
Sequence Alignment
Mafft
Prank
Muscle
hmmer
Macse
Diamond
Blast+
LASTZ
BLAT
Model Selection
Estimate phylogenies
Garli
RAxML
RAxML-ng
MrBayes
ExaML
ExaBayes
Astral
BEAST
IQ-TREE
Phylogeny and Statistical Visualization (Python modules & R libraries)
Toytree
ETE Toolkit
iTOL
Toyplot
ggtree
Matplotlib
Seaborn
Bokeh
ggplot (for Python)
pygg
plotnine
ipyvega
Sequence Simulation
NGS Read Visualization and Quality Control
FASTX-Toolkit
FASTQC
Trimmomatic
PRINSEQ
NGS Error Correction
NGS Short-Read Aligners
- see this post for an old but good discussion on read mapping to generate a consensus
NGS Read Alignment Manipulation
Genome Manipulation Tools
Transcriptome Assembly
Trinity
Velvet
SOAPdenovo-Trans
Genome Assembly
SOAPdenovo2
ALLPATHS-LG
DISCOVAR de novo
SPAdes
Genome Annotation
Orthology inference (tree-based and sequence similarity-based)
Yang and Smith 2014
Orthograph
OMA
OrthoSelect
HaMStR
OrthoMCL
Agalma
Geo Mapping
Basemap Maplotlib Toolkit
Bokeh
Vincent