CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages
macros.xml
lineage_report.tsv
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additional['write_tree']
`_.
To do this, Pangolin employs the use of external programs including: `iqtree `_, `mafft `_,
and `snakemake `_.
More information can be obtained from the authors github site: https://github.com/hCoV-2019/pangolin
You may also wish to visit the authors website at https://pangolin.cog-uk.io/
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**Input** - Multi sequence fasta file or individual fasta files
**Output** - lineage report:
+---------+---------+------+-------------+------------------+-----------+-----------+
| Taxon | Lineage | aLRT | UFbootstrap | lineages_version | status | note |
+=========+=========+======+=============+==================+===========+===========+
| Sample1 | A.1 | 100 | 60 | 2020-04-27 | passed_qc | |
+---------+---------+------+-------------+------------------+-----------+-----------+
| Sample2 | B.1 | 80 | 80 | 2020-04-27 | passed_qc | |
+---------+---------+------+-------------+------------------+-----------+-----------+
| Sample3 | B.1.4 | 60 | 100 | 2020-04-27 | fail | seq_len:0 |
+---------+---------+------+-------------+------------------+-----------+-----------+
Resources for interpreting aLRT and UFbootstrap values:
- `IQ_TREE: Assessing branch supports with single branch tests `_
- `IQ_TREE: Command Reference `_
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