macmanes-lab / PAML
This is code for running Orthofinder -> PAML
☆12Updated 8 years ago
Related projects ⓘ
Alternatives and complementary repositories for PAML
- Generating UTRs from SHort Reads☆11Updated 4 years ago
- Add multiple thread function for genome comparison☆15Updated 3 years ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Updated 5 years ago
- BUSCOMP: BUSCO Compiler and Comparison tool☆21Updated 2 months ago
- CAAStools is a bioinformatics toolbox that allows the user to identify and validate CAAS on MSA of orthologous proteins.☆14Updated last year
- TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to majo…☆12Updated 4 years ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆23Updated 2 years ago
- ☆19Updated 3 months ago
- Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.☆29Updated 6 years ago
- Domain based annotation of transposable elements☆19Updated last month
- Data analysis of Funannotate and Orthofinder outputs to Pangenome results☆17Updated 4 years ago
- ☆16Updated 2 years ago
- Plant genome assembly and annotation pipeline using snakemake☆35Updated last year
- Genome alignment and synteny plots☆27Updated last year
- Scripts for NGS processing☆17Updated 7 years ago
- Scripts used to perform analyses in Rice et al. (2023)☆14Updated 10 months ago
- Genome Annotation Pipeline☆32Updated 3 months ago
- Calculate circos format data of GC content and GC skew from genome data.☆11Updated 9 years ago
- The MafFilter genome alignment processor☆17Updated 2 months ago
- Pathway Tools multiprocessing wrapper (for PathoLogic).☆15Updated 7 months ago
- ☆22Updated last year
- A high performance tool to identify orthologs and paralogs across genomes.☆27Updated last year
- a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees☆24Updated 5 months ago
- a broadly applicable tool for automated gene identification and retrieval☆28Updated 4 months ago
- Simple tools for working with Hi-C data☆16Updated 5 years ago
- This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new trans…☆17Updated 4 months ago
- ☆21Updated 5 years ago
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- An R package to infer and analyze synteny networks from protein sequences☆21Updated last month
- A Python package for testing evolutionary hypotheses in genome-wide approaches.☆31Updated 3 years ago