Computational Biology Laboratory

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33 repositories

CompressSequences
Public
How compressible are sequences?
Shell
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
OptimJV3
Public
Optimize compression parameters of Jarvis3
Shell
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GNU General Public License v3.0
•0•1•0•0•Updated Oct 31, 2024Oct 31, 2024
jarvis3
Public
Efficient compression of biological data
dna data-compression dna-sequences
C
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GNU General Public License v3.0
•0•3•0•0•Updated Oct 28, 2024Oct 28, 2024
ac2
Public
An efficient amino acid sequence compressor using Neural Networks
protein-sequences data-compression algorithms-and-data-structures
C
•
GNU General Public License v3.0
•3•6•0•0•Updated Oct 21, 2024Oct 21, 2024
altair
Public
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data
toolkit data-analysis data-compression alignment-free temporal-analysis
C
•
GNU General Public License v3.0
•0•4•0•0•Updated Sep 2, 2024Sep 2, 2024
alcor
Public
Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data
toolkit information-theory data-analysis alignment-free data-complexity bioinformatics simulation
C
•
GNU General Public License v3.0
•1•10•0•0•Updated Jul 9, 2024Jul 9, 2024
HumanGenome
Public
How compressible is a human genome sequence?
benchmark data-compression human-genome
Shell
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GNU General Public License v3.0
•1•5•0•0•Updated May 15, 2024May 15, 2024
spark
Public
This program schools, simulates, and searches for exact or approximate Turing Machines (TMs) with specific characteristics.
information-theory turing-machine algorithms-and-data-structures
C
•
GNU General Public License v3.0
•1•1•0•0•Updated May 2, 2024May 2, 2024
cryfa
Public
A secure encryption tool for genomic data
genomics fastq-format fasta-format encryption keygen compact
C++
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GNU General Public License v3.0
•14•56•0•0•Updated Apr 14, 2024Apr 14, 2024
geco2
Public
An improved compression tool for DNA sequences
computational-biology dna data-compression dna-sequences genomic dna-compression
C
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GNU General Public License v3.0
•2•9•0•0•Updated Mar 22, 2024Mar 22, 2024
OAWK
Public
Shell
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GNU General Public License v3.0
•0•1•0•0•Updated Mar 11, 2024Mar 11, 2024
FASTA-ANALYSIS
Public
Sorting of DNA sequences within a Multi-Fasta file
Shell
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GNU General Public License v3.0
•0•1•0•0•Updated Feb 22, 2024Feb 22, 2024
magnet
Public
An ultra-fast and high-sensitive tool to filter specific DNA content
data-compression magnet exogenous alignment-free ancient-dna-sequences endogenous ancient-genomes
C
•
GNU General Public License v3.0
•2•2•0•1•Updated Feb 21, 2024Feb 21, 2024
MizaR
Public
A sorting method for encoding metagenomic data
sorting data-compression fastq-files
Shell
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GNU General Public License v3.0
•0•1•0•0•Updated Nov 7, 2023Nov 7, 2023
cpm-fcm
Public
An encoder for biological sequences using Copy Models and Finite-context models
data-compression biological-sequences
GNU General Public License v3.0
•0•2•0•0•Updated Nov 6, 2023Nov 6, 2023
gto
Public
A genomics-proteomics toolkit
C
•
MIT License
•12•46•0•1•Updated Oct 18, 2023Oct 18, 2023
falcon
Public
A tool to infer metagenomic sample composition
metagenomics compression-algorithm alignment-free ancient-dna-sequences ancientdna falcon-meta falcon
C
•
GNU General Public License v3.0
•7•21•0•0•Updated Oct 10, 2023Oct 10, 2023
jarvis2
Public
Efficient DNA sequence compression
data-compression algorithms-and-data-structures genomic-sequences jarvis2
C
•
GNU General Public License v3.0
•3•3•0•0•Updated Jul 13, 2023Jul 13, 2023
CassavaGenome
Public
How compressible is a Cassava genome sequence?
benchmark data-compression cassava-genome
Shell
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GNU General Public License v3.0
•1•2•0•0•Updated May 30, 2023May 30, 2023
SynTegra
Public
A computational tool for simulation of viral synthetic integrations
C
•
GNU General Public License v3.0
•0•1•0•0•Updated Mar 15, 2023Mar 15, 2023
cobilab.github.io
Public
Cobilab website
website cobilab
CSS
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MIT License
•1•2•0•0•Updated Feb 23, 2023Feb 23, 2023
jarvis
Public
Efficient lossless compression of genomic sequences
genome-compression compression jarvis
C
•
GNU General Public License v3.0
•3•8•0•0•Updated Jan 25, 2023Jan 25, 2023
geco3
Public
An efficient DNA sequence compressor using Neural Networks
neural-networks compression-algorithm dna-sequences
C
•
GNU General Public License v3.0
•8•12•1•0•Updated Jan 25, 2023Jan 25, 2023
RFSC
Public
Reference-Free Sequence Classification Tool for DNA sequences in metagenomic samples
Shell
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GNU General Public License v3.0
•4•4•1•0•Updated Jun 9, 2022Jun 9, 2022
evo
Public
Evolutionary patterns in SARS-CoV-2 genomes
C
•
GNU General Public License v3.0
•0•1•0•0•Updated Jul 29, 2021Jul 29, 2021
nn-expert-mixer
Public
C++
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GNU General Public License v3.0
•1•1•0•0•Updated Nov 30, 2020Nov 30, 2020
eagle
Public
An ultra-fast tool to find relative absent words in genomic data
C
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GNU General Public License v3.0
•6•5•0•0•Updated Jul 30, 2020Jul 30, 2020
smashpp
Public
Find and visualize rearrangements in DNA sequences
C++
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GNU General Public License v3.0
•13•2•0•0•Updated Jun 16, 2020Jun 16, 2020
chester
Public
A memory efficient tool to map and visualize evolutionary regions
visualization singularity alignment-free variation evolutionary-regions chester
C
•
GNU General Public License v3.0
•1•6•0•1•Updated Mar 11, 2020Mar 11, 2020
ac
Public
A lossless compression tool for Amino Acid sequences
ac protein-compression compression amino-acid-compression
C
•
GNU General Public License v3.0
•3•4•0•0•Updated Jan 29, 2020Jan 29, 2020