sequence-alignments

There are 1 repository under sequence-alignments topic.

tanghaibao / jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
allmaps assembly bioinformatics blast comparative-genomics genetic-maps genome-sequencing genomics sequence-alignments synteny variant-calling
Language:Python 701
seqan / seqan
SeqAn's official repository.
cpp14 bioinfomatics high-performance simd sequence-alignments alignment bwt indexing suffixarray htslib sam-bam fasta fastq-format blast seqan
Language:C++ 458
walaj / SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
bwa-mem c-plus-plus fermi htslib sequence-alignments
Language:C++ 133
debbiemarkslab / plmc
Inference of couplings in proteins and RNAs from sequence variation
protein-interaction protein-sequences protein-structure sequence-alignments undirected-graphs
Language:C 96
drostlab / orthologr
Genome wide orthology inference and dNdS estimation
blast-searches orthology-inference comparative-genomics-studies genomics sequence-alignments blast comparative dnds-estimation codon-alignment r entire-genomes orthologous-genes biomartr species comparing-genomes genomics-studies retrieve-genomes comparative-genomics proteome sequence-alignment
Language:R 84
pymodproject / pymod
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
pymol bioinformatics sequence-alignments structural-alignments homology-modeling similarity-searches pymol-plugin protein-structures protein-sequences
Language:Python 71
MACSE_V2_PIPELINES
ranwez / MACSE_V2_PIPELINES
This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
bioinformatics-pipeline barcoding sequence-alignment sequence-alignments singularity-container nextflow
Language:Shell 28
humanlongevity / tredparse
TREDPARSE: HLI Short Tandem Repeat (STR) caller
genomics genetic-analysis sequence-alignments genome-sequencing genome-annotation
Language:Python 24
laurentnoe / yass
genomic alignment similarity search tool
sequence-alignment spaced-seed dna-sequences fasta-sequences fasta genomic-data-analysis blastn blast-search sequence-alignments align-dna-sequences
Language:C 18
benhid / Sequoya
Solving Multiple Sequence Alignment (MSA) problems with multi-objective metaheuristics
metaheuristics msa multiple-sequence-alignment optimization python sequence-alignments
Language:Python 17
wafflespeanut / nucleic-acid
BWT, FM-index and bits vector for analyzing DNA sequence data.
dna sequence-alignments bioinformatics bwt rust
Language:Rust 17
benhid / NeedlemanWunschPy
This code is meant for educational purposes only! Sequence alignment in Python 3.x using Needleman–Wunsch algorithm. Reference code from TyMA (2017 - University of Málaga)
bioinformatics needleman-wunsch sequence-alignments
Language:Python 5
mohammadtavakoli78 / Bioinformatics
This is projects of Bioinformatics
msa multiple-sequence-alignment profile sequence-alignment sequence-alignments star-algorithm
Language:Python 5
akiomiyao / ped
Polymorphic Edge Detection - An efficient polymorphism detector for NGS data
polymorphism inversion insertion ngs deletion snp k-mer ngstools alignment-free-algorithm somatic-mutations genotype sequence-alignments variant cnv copy-number-variation crispr-cas9
Language:Perl 4
ggirelli / ood-fish
Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)
dna dna-sequences barcode barcodes sequence sequence-alignments dimerization free-energy thermodynamics sequencing blat pmc clique graph-theory
Language:R 4
jeanmanguy / multi-seq-align
A crate to manipulate multiple sequences alignments in Rust.
bioinformatics rustlang msa sequence-alignments evolution
Language:Rust 4
josejimenezluna / odseq
Outlier detection in multiple sequence alignment
bioinformatics sequence-alignments outlier-detection
Language:R 4
kyungtaekLIM / arelia
Reliability Scoring and Masking of Multiple Sequence Alignments
sequence-alignments
Language:Python 2
laurentnoe / iedera
subset and spaced seed design tool
sequence-alignment indexing spaced-seed read-mapping alignment-free metagenomic-classification sequence-alignments k-mer align
Language:C++ 2
kevinah95 / bmc-sequence-alignment
El presente trabajo muestra la aplicación de algoritmos de alineación de secuencias conocidos como needleman-wunsch (global), smith-waterman (local) y semi-global con sus variantes (kband o afín de costo por gap).
bioinformatics needleman-wunsch smith-waterman semiglobal sequence-alignments
Language:Python 1
nurhafiza / DSA
Differential Search Algorithm for Gene Sequence Assembly
dsa sequence-assembler sequence-alignments matlab-codes
Language:MATLAB 1
nurhafiza / FA
Firefly Algorithm for Gene Sequence Assembly
firefly-algorithm sequence-assembler sequence-alignments matlab-codes
Language:MATLAB 1
nurhafiza / FADSA
A New Hyper-Heuristic Algorithm (FADSA) for Gene Sequence Assembly
hyper-heuristic sequence-assembler sequence-alignments matlab-codes
Language:MATLAB 1
salilab / mdt
Generate frequency tables used by Modeller and IMP.
protein-structure statistics sequence-alignments
Language:C 1
kyungtaekLIM / seqlim
Easy Manipulation of Multiple Sequence Alignments (Concatenation and Format Conversion)
fasta nexus phylip msa sequence-alignments
Language:Python 0
liorzoue / dna-seq
dna sequence-alignments batch fasta fastq-format alignment
Language:C# 0
ggirelli / seq-lib-gg
Base librarys for sequencing data analysis.
sequence sequence-alignments sequence-to-sequence sequence-alignment sequence-search library base analysis sequencing
Language:R
weng-lab / bam-aggregate-task
Kotlin task for aggregating reads from a BAM file across a set of genomic regions
bioinformatics sequence-alignments aggregation footprinting
Language:Kotlin