alignment-free
There are 41 repositories under alignment-free topic.
smortezah/smashpp
Find and visualize rearrangements in DNA sequences
EvolBioInf/andi
♥ Efficient Estimation of Evolutionary Distances
shahab-sarmashghi/Skmer
Fast and accurate tool for estimating genomic distances between genome-skims
TurtleTools/geometricus
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
EvolBioInf/phylonium
♥ Fast and Accurate Estimation of Evolutionary Distances
cobilab/falcon
A tool to infer metagenomic sample composition
AlgoLab/shark
Mapping-free software for fishing relevant reads in an RNA-Seq sample
bhi-kimlab/DeepFam
Deep learning based alignment-free method for protein family modeling and prediction
Angknpng/SACNet
Alignment-Free RGBT Salient Object Detection: Semantics-guided Asymmetric Correlation Network and A Unified Benchmark
BioinformaticsToolsmith/MeShClust2
MeShClust2: Application of alignment-free identity scores in clustering long DNA sequences
cobilab/alcor
Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data
AlgoLab/malva
genotyping by Mapping-free ALternate-allele detection of known VAriants
cobilab/altair
AltaiR: a C toolkit for alignment-free and temporal analysis of multi-FASTA data
bioinfoUQAM/CASTOR_KRFE
Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences
cobilab/geco
A tool for compression and analysis of DNA sequences
CNuge/alfie
A neural network for alignment-free, kingdom-level classification of eDNA
moorembioinfo/KmerAperture
Extract SNPs and accessory differences in closely related bacterial genomes from k-mers
cobilab/chester
A memory efficient tool to map and visualize evolutionary regions
IQTLabs/librtd
Generalized k-mer return time distribution (RTD) calculation library
raghavagps/transfacpred
An ensemble method for predicting transcription factor in protein sequences
BioinformaticsToolsmith/Alignment-Free-Kmer-Statistics
Supplementary data for "A survey and evaluations of histogram-based statistics in alignment-free sequence comparison"
gi-bielefeld/sans
Alignment-free phylogenomic splits
tdencker/multi-SpaM
Phylogeny reconstruction based on spaced word matches
Angknpng/PCNet
Alignment-Free RGB-T Salient Object Detection: A Large-scale Dataset and Progressive Correlation Network
BioinformaticsToolsmith/FASTCAR
Fast and Accurate Search Tool for Classification And Regression in global sequence similarity
bioinfoUQAM/Caribou
Alignment-free bacterial identification and classification in metagenomics sequencing data using machine learning
GenGrim76/Pareto-Optimal-GDC
:chart_with_downwards_trend: Disk Storage of Compressed k-mer Dictionaries, with or without Random Access in Main Memory.
laurentnoe/iedera
subset and spaced seed design tool
AlgoLab/MALVIRUS
A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)
cobilab/magnet
An ultra-fast and high-sensitive tool to filter specific DNA content
rhpvorderman/fastqdedup
Alignment-free FASTQ deduplication.
sirineFoudili/DNA-comparison-and-alignment-
web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.
CamilaPPerico/rSWeeP
rSWeeP is an alignment-free method for the vector representation of the biological sequences (amino acid and nucleotide).
enai4bio/Xlassify
An alignment-free deep-learning model trained to classify human gut bacteria
MsAlEhR/Scorpio
Scorpio: Advancing Embeddings for Superior Biological Sequence Analysis
smortezah/phd
My PhD thesis