Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: alignment-free

raghavagps/transfacpred

An ensemble method for predicting transcription factor in protein sequences

Language: Python - Size: 172 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 1

EvolBioInf/phylonium

♥ Fast and Accurate Estimation of Evolutionary Distances

Language: C++ - Size: 855 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 25 - Forks: 5

laurentnoe/iedera

subset and spaced seed design tool

Language: C++ - Size: 1.26 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 2 - Forks: 1

TurtleTools/geometricus

A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

Language: Jupyter Notebook - Size: 12.9 MB - Last synced: 16 days ago - Pushed: 12 months ago - Stars: 34 - Forks: 8

smortezah/smashpp

Find and visualize rearrangements in DNA sequences

Language: C++ - Size: 760 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 56 - Forks: 12

AlgoLab/malva

genotyping by Mapping-free ALternate-allele detection of known VAriants

Language: C - Size: 19.4 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 9 - Forks: 4

EvolBioInf/andi

♥ Efficient Estimation of Evolutionary Distances

Language: C - Size: 7.22 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 34 - Forks: 14

cobilab/geco

A tool for compression and analysis of DNA sequences

Language: C - Size: 338 KB - Last synced: 4 months ago - Pushed: over 7 years ago - Stars: 8 - Forks: 5

cobilab/chester

A memory efficient tool to map and visualize evolutionary regions

Language: C - Size: 1.57 MB - Last synced: 4 months ago - Pushed: about 4 years ago - Stars: 6 - Forks: 1

cobilab/alcor

Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data

Language: C - Size: 557 MB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 9 - Forks: 1

moorembioinfo/KmerAperture

Extract SNPs and accessory differences in closely related bacterial genomes from k-mers

Language: Python - Size: 986 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 0

shahab-sarmashghi/Skmer

Fast and accurate tool for estimating genomic distances between genome-skims

Language: Python - Size: 4.61 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 32 - Forks: 7

cobilab/magnet

An ultra-fast and high-sensitive tool to filter specific DNA content

Language: C - Size: 346 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 2

bhi-kimlab/DeepFam

Deep learning based alignment-free method for protein family modeling and prediction

Language: Python - Size: 3.04 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 16 - Forks: 8

AlgoLab/shark

Mapping-free software for fishing relevant reads in an RNA-Seq sample

Language: C++ - Size: 30.3 MB - Last synced: about 2 months ago - Pushed: over 3 years ago - Stars: 18 - Forks: 1

cobilab/falcon

A tool to infer metagenomic sample composition

Language: C - Size: 29.1 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 21 - Forks: 7

bioinfoUQAM/CASTOR_KRFE

Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences

Language: Python - Size: 2.89 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 9 - Forks: 2

GenGrim76/Pareto-Optimal-GDC

:chart_with_downwards_trend: Disk Storage of Compressed k-mer Dictionaries, with or without Random Access in Main Memory.

Language: Java - Size: 66.4 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

IQTLabs/librtd 📦

Generalized k-mer return time distribution (RTD) calculation library

Language: Nim - Size: 594 KB - Last synced: 7 days ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1

cobilab/altair

AltaiR: a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data

Language: C - Size: 206 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

AlgoLab/MALVIRUS

A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)

Language: JavaScript - Size: 5.87 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2

CNuge/alfie

A neural network for alignment-free, kingdom-level classification of eDNA

Language: Python - Size: 41.5 MB - Last synced: 24 days ago - Pushed: about 2 years ago - Stars: 7 - Forks: 3

bioinfoUQAM/Caribou

Alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning

Language: Python - Size: 9.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 1

rdmpage/dimacs-dnabarcode-challenge

Files from DIMACS 2007 DNA barcoding challenge

Language: C - Size: 16.2 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

maremita/CASTOR_KRFE_v1.0

[Features extraction method] You can find the new version of CASTOR_KRFE at https://github.com/bioinfoUQAM/CASTOR_KRFE

Language: Python - Size: 1.94 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

rhpvorderman/fastqdedup

Alignment-free FASTQ deduplication.

Language: C - Size: 147 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

BioinformaticsToolsmith/MeShClust2

MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences

Language: C++ - Size: 184 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 11 - Forks: 0

BioinformaticsToolsmith/Alignment-Free-Kmer-Statistics

Supplementary data for "A survey and evaluations of histogram-based statistics in alignment-free sequence comparison"

Language: C++ - Size: 723 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 3 - Forks: 1

BioinformaticsToolsmith/FASTCAR

Fast and Accurate Search Tool for Classification And Regression in global sequence similarity

Language: C++ - Size: 4.78 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 3 - Forks: 2

amatur/CRISPR-nRef-gRNA-Design

Language: Shell - Size: 43.9 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

Related Keywords
alignment-free 30 bioinformatics 12 machine-learning 4 kmers 3 genotyping 2 data-analysis 2 virus-classification 2 taxonomic-classification 2 dna-sequences 2 toolkit 2 genomics 2 svm-rfe 2 svm 2 rfe 2 compression 2 ancient-dna-sequences 2 castor-krfe 2 castor 2 k-mer 2 compression-algorithm 2 computational-biology 2 deep-learning 2 pareto-optimality 1 random-access-in-main-memory 1 succinct-data-structure 1 nim 1 genomics-data 1 compressor 1 feature-extraction 1 metagenomics 1 falcon-meta 1 falcon 1 ancientdna 1 rna-seq 1 k-mer-counting 1 grna-sequence 1 crispr 1 candidate-selection 1 sequence-clustering 1 bioinformatics-tool 1 alignment-free-algorithm 1 umi 1 hamming-distance 1 hamming 1 fastq 1 deduplication 1 kmer-extraction 1 dna-barcoding 1 dna 1 classification-models 1 bacterial-genomes 1 bacteria-classification 1 python 1 neural-network 1 virology 1 sars-cov-2 1 kmer 1 genotyping-by-sequencing 1 spatial-temportal 1 nim-lang 1 vcf 1 ngs 1 high-throughput-sequencing 1 genome-rearrangment 1 genome-compression 1 data-visualization 1 proteins 1 protein-structure 1 invariant-features 1 feature-engineering 1 spaced-seed 1 sequence-alignments 1 sequence-alignment 1 read-mapping 1 metagenomic-classification 1 indexing 1 align 1 phylogenetics 1 transcription-factors 1 machine-learning-algorithms 1 hybrid-approach 1 blast 1 filtering 1 protein-sequence 1 convolutional-neural-networks 1 magnet 1 exogenous 1 endogenous 1 data-compression 1 ancient-genomes 1 genome-skims 1 estimating-genomic-distances 1 assembly-free 1 snps 1 simulation 1 information-theory 1 data-complexity 1 visualization 1 variation 1 singularity 1