| BLAST |
BLAST (basic local alignment search tool) is an algorithm for comparing primary
biological sequence information, such as the amino-acid sequences of proteins or
the nucleotides of DNA and/or RNA sequences. |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
2.6.0 |
|
| Species Identification |
BLAST (basic local alignment search tool) is an algorithm for comparing primary
biological sequence information, such as the amino-acid sequences of proteins or
the nucleotides of DNA and/or RNA sequences. |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
2.6.0 |
|
| Sequences Fetch |
Samtools is a suite of programs for interacting with high-throughput sequencing data. |
https://www.htslib.org/ |
0.1.19 |
Heng Li |
| Phylogenetic tree |
MUSCLE is one of the best-performing multiple alignment programs according to
published benchmark tests, with accuracy and speed that are consistently better
than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users
learn everything they need to know about MUSCLE in a few minutes—only a handful
of command-line options are needed to perform common alignment tasks. |
http://www.drive5.com/muscle/ |
3.8.31 |
|
| Genewise |
GeneWise compares a protein sequence to a genomic DNA sequence, allowing for
introns and frameshifting errors. |
|
wise2-4-1 |
|
| Colinearity |
This document describes installation and usage of the LASTZ sequence alignment
program. LASTZ is a drop-in replacement for BLASTZ, and is backward compatible
with BLASTZ's command-line syntax. That is, it supports all of BLASTZ's options
but also has additional ones, and may produce slightly different alignment
results. |
http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/_README.lastz-1.02.00.html |
1.02.00 |
Bob Harris |
| Primer Design |
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction").
PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also
design hybridization probes and sequencing primers.
|
https://primer3.ut.ee/ |
4.1.0 |
| OGDRAW |
OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The
input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files.
The application is optimized to create detailed high-quality maps of organellar genomes (plastid and
mitochondria). Nevertheless, you can upload most database entries.
|
https://chlorobox.mpimp-golm.mpg.de/OGDraw.html |
v.1.1.1 |