rcedgar

Pinned Repositories

muscle
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
Language:C++186 6 7121
newick
Manipulate and generate figures for trees in Newick format
Language:C++18 2 51
palmdb
Database of virus RdRP barcode sequences
15 3 45
palmscan
Language:C++25 3 25
reseek
Protein structure alignment and search algorithm
Language:C++23 2 43
spades_circular_contigs
Python script to identify circular contigs from SPAdes assembler.
Language:Python7 2 01
syncmer
Validation of sycnmers compared to minimizers
Language:C++11 3 04
urmap
URMAP ultra-fast read mapper
Language:C++39 4 911
usearch12
Open-source usearch
Language:C++69 4 116
usearch_old_binaries
Executable files for usearch versions 5 through 11, donated to the public domain
7 1 02

rcedgar's Repositories

rcedgar/muscle
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
Language:C++186 6 7121
rcedgar/usearch12
Open-source usearch
Language:C++69 4 116
rcedgar/palmscan
Language:C++25 3 25
rcedgar/reseek
Protein structure alignment and search algorithm
Language:C++23 2 43
rcedgar/newick
Manipulate and generate figures for trees in Newick format
Language:C++18 2 51
rcedgar/palmdb
Database of virus RdRP barcode sequences
15 3 45
rcedgar/syncmer
Validation of sycnmers compared to minimizers
Language:C++11 3 04
rcedgar/spades_circular_contigs
Python script to identify circular contigs from SPAdes assembler.
Language:Python7 2 01
rcedgar/usearch_old_binaries
Executable files for usearch versions 5 through 11, donated to the public domain
7 1 02
rcedgar/palm_annot
Scripts, HMMs and search databases for identifying and classifying viral RdRp sequences
Language:Python5 2 32
rcedgar/rdrp_tree_experiments
Code, data and results for Muscle5 ensemble experiments on RdRp genus and phylum trees
Language:Roff5 1 00
rcedgar/renomad
Implementation of NOMAD (https://doi.org/10.1101/2022.06.24.497555)
Language:C++4 1 20
rcedgar/circuclust
Clustering and alignment for circular sequences
Language:C++3 1 00
rcedgar/palmscan2
Language:C++3 2 0
rcedgar/jupiter
Generate "Jupiter" plots for circular genomes
Language:Python2 2 0
rcedgar/re_coding_style
Robert C. Edgar's C++ coding style
2 1 0
rcedgar/balifam
Protein multiple sequence alignment benchmark
1 2 11
rcedgar/pylddt
Python script to calculate LDDT and DALI Z score from MSA plus structures
Language:Python1
rcedgar/qscore
Compares a multiple alignment with a reference and reports accuracy scores.
Language:C1 2 03
rcedgar/retree
Python Newick tree format parser and Robinson-Foulds calculator (self-teaching exercise)
Language:Python1 1 0
rcedgar/tara_oceans
Data and scripts to reproduce my analysis of Tara Oceans data
Language:Python1 2 0
rcedgar/usearch12_documentation
Documentation for USEARCH v12
Language:HTML1 2 01
rcedgar/cmpairs
Parse infernal cmscan tbl file to find pairs of hits to same model on different strands
Language:Python2 0
rcedgar/diamond
Accelerated BLAST compatible local sequence aligner.
Language:C++1 0
rcedgar/HelloWorld
A C++ Hello World project, using CMake, and GitHub Actions
Language:CMake1 0
rcedgar/muscle_benchmark
Language:Python
rcedgar/regammon
RE-implementation of TD-Gammon
Language:C1 0
rcedgar/reseek_scop40
Language:Python2 0
rcedgar/ribozy
Code for identifying candidate ribozyviria sequences
Language:Python1 0
rcedgar/vcxproj2makefile
Simple python2 script to convert Microsoft Visual Studio C++ project to gcc Makefile
Language:Python2 02