diff --git a/README.md b/README.md index 5916c44..d989bee 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ conda install tipars2 # Quick Usage -## Pango lineage annotation +## Ancestral lineage annotation ```bash cd /home/ytye/tipars2_github/Benchmark_datasets/100k @@ -52,20 +52,20 @@ cd /home/ytye/tipars2_github/Benchmark_datasets/100k ## Tree refinement ### Phylogenetic insertion using TIPars -+ include processing tree annotation ++ include processing ancestral lineage annotation ```bash cd /home/ytye/tipars2_github/Benchmark_datasets/100k /home/ytye/tipars2_github/tipars2 --refinement -t 100k_tree_InnodeNameAdded.nwk -s 100k_taxa.fas -a 100k_anc.fas --label 100k_pangolin.tsv --output refined_tree.nwk -T 8 -x 8G ``` -+ exclude processing tree annotation that could be computed by other methods, e.g. PastML and matUtils ++ exclude processing ancestral lineage annotation that could be computed by other methods, e.g. PastML and matUtils ```bash cd /home/ytye/tipars2_github/Benchmark_datasets/100k /home/ytye/tipars2_github/tipars2 --refinement_from_annotation -t 100k_tree_InnodeNameAdded.nwk -s 100k_taxa.fas -a 100k_anc.fas --label 100k_pangolin.tsv --assignment 1248_in_100k_annotation.tsv --output refined_tree.nwk -T 8 -x 8G ``` ### Phylogenetic insertion using UShER -+ use the [#consistent_taxa]_removedTree.nwk after tree annotation by TIPars2 ++ use the [#consistent_taxa]_removedTree.nwk after ancestral lineage annotation by TIPars2 ```bash cd /home/ytye/tipars2_github/Benchmark_datasets/100k /home/ytye/tipars2_github/tipars2 --annotation -t 100k_tree_InnodeNameAdded.nwk --label 100k_pangolin.tsv --output 1248_in_100k_annotation.tsv -T 8 @@ -80,7 +80,7 @@ usher -v taxa.vcf -t 81784_removedTree.tree -d ./usher -o ./usher/81784_AddTo_10 # Acknowledgements -This project is supported by the Hong Kong Research Grants Council General Research Fund (17150816), the NSFC Excellent Young Scientists Fund (Hong Kong and Macau) (31922087), +This project is supported by the Theme Based Research Scheme (T11-705/21-N), the Hong Kong Research Grants Council General Research Fund (17150816), the NSFC Excellent Young Scientists Fund (Hong Kong and Macau) (31922087), the Health and Medical Research Fund (COVID1903011-549 WP1) and the Innovation and Technology Commission’s InnoHK funding (D24H).