Pinned Repositories
allele-specific-expression
Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)
angsd
Program for analysing NGS data.
ASTER
Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)
cactus
Official home of genome aligner based upon notion of Cactus graphs
CKMedoidsTreeClustering
A new fast method for building multiple consensus trees using k-medoids
Comparative-Annotation-Toolkit
CSA
Cyclic DNA Sequence Aligner
CSAVanalysis
This analysis aims to detect convergent single amino acid variants among species from polyphyletic clades
Fruf_v1_assembly
The genome assembly pipeline for Fulvetta ruficapilla.
PolarizePigAncestralAlleles
YanCheer's Repositories
YanCheer/PolarizePigAncestralAlleles
YanCheer/Fruf_v1_assembly
The genome assembly pipeline for Fulvetta ruficapilla.
YanCheer/angsd
Program for analysing NGS data.
YanCheer/ASTER
Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)
YanCheer/cactus
Official home of genome aligner based upon notion of Cactus graphs
YanCheer/Comparative-Annotation-Toolkit
YanCheer/CSAVanalysis
This analysis aims to detect convergent single amino acid variants among species from polyphyletic clades
YanCheer/FalseDuplication
false duplication and false gene gain research for VGP assemblies.
YanCheer/FriendsDontLetFriends
Friends don't let friends make certain types of data visualization - What are they and why are they bad.
YanCheer/gotree
Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.
YanCheer/HOTFOXES
Scripts for Rocha et al. 2023: "North-African fox genomes show signatures of repeated introgression and adaptation to life in deserts"
YanCheer/HQGR
The High Quality Reads Generator (HQGR) script is provided to implement second round of CCS for long amplicon HiFi sequencing.
YanCheer/Kakapo
Scripts and code for Kākāpō genomic data
YanCheer/LoCSI-for-non-model-species
YanCheer/MA
The Modular Aligner and The Modular SV Caller
YanCheer/mafTools
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
YanCheer/paleomix
Pipelines and tools for the processing of ancient and modern HTS data.
YanCheer/PhyKIT
a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies
YanCheer/phylociraptor
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
YanCheer/pixy
Software for painlessly estimating average nucleotide diversity within and between populations
YanCheer/raxml-ng
RAxML Next Generation: faster, easier-to-use and more flexible
YanCheer/read2tree
a tool for inferring species tree from sequencing reads
YanCheer/RepeatMasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
YanCheer/rotate
simple program to rotate a circular sequence to start at a given position or string
YanCheer/sequenceTools
YanCheer/SLD_Admix
YanCheer/SolEvo_PotatoDele
Use hifi to assembly the Sol genome, and dissecting Sol evo
YanCheer/twisst
Topology weighting by iterative sampling of sub-trees
YanCheer/verkko
YanCheer/vgp-assembly
VGP repository for the genome assembly working group