1. What is the input of PhySpeTree?
-
Users only need to prepare a TXT file containing KEGG abbreviated species names. For example, organism_example_list.
-
Now, PhySpeTree not only supported the user input three- or four-letter organism codes (KEGG database organism codes) but also the NCBI taxonomy id (for example human taxonomy id is 9606). You can search taxonomy id form NCBI taxonomy database.
2. How to explain PhySpeTree outputs?
PhySpeTree returns two folders, Outdata contains the output species tree and temp includes temporary data. Files in temp can be used to check the quality of outputs in each step. If HCP method (--hcp) is selected, the temp folder includes:
conserved_protein: highly conserved proteins retrieved from the KEGG database.alignment: aligned sequences.concatenate: concatenated sequences and conserved blocks.
If SSU rRNA method (--srna) is selected, the temp folder includes:
rna_sequence: SSU rRNA sequences retrieved from the SILVA database.rna_alignment: aligned sequences and conserved blocks.
3. What classes of HCP are selected?
PhySpeTree uses 31 HCP without horizontal transferred genes according to Ciccarelli et al..
cite:
Ciccarelli FD, Doerks T, Von Mering C, et al. Toward automatic reconstruction of a highly resolved tree of life[J]. science, 2006, 311(5765): 1283-1287.
The 31 HCP and corresponding KEGG KO number are shown in the following table:
| Protein Names | Eukaryotes KO | Prokaryotes KO |
|---|---|---|
| DNA-directed RNA polymerase subunit alpha | K03040 | K03040 |
| Ribosomal protein L1 | K02865 | K02863 |
| Leucyl-tRNA synthetase | K01869 | K01869 |
| Metal-dependent proteases with chaperone activity | K01409 | K01409 |
| Phenylalanine-tRNA synthethase alpha subunit | K01889 | K01889 |
| Predicted GTPase probable translation factor | K06942 | K06942 |
| Preprotein translocase subunit SecY | K10956 | K10956 |
| Ribosomal protein L11 | K02868 | K02867 |
| Ribosomal protein L13 | K02873 | K02871 |
| Ribosomal protein L14 | K02875 | K02874 |
| Ribosomal protein L15 | K02877 | K17437 |
| Ribosomal protein L16/L10E | K02866 | K02872 |
| Ribosomal protein L18 | K02883 | K02882 |
| Ribosomal protein L22 | K02891 | K02890 |
| Ribosomal protein L3 | K02925 | K02906 |
| Ribosomal protein L5 | K02932 | K02931 |
| Ribosomal protein L6P/L9E | K02940 | K02939 |
| Ribosomal protein S11 | K02949 | K02948 |
| Ribosomal protein S15P/S13E | K02958 | K02956 |
| Ribosomal protein S17 | K02962 | K02961 |
| Ribosomal protein S2 | K02981 | K02967 |
| Ribosomal protein S3 | K02985 | K02982 |
| Ribosomal protein S4 | K02987 | K02986 |
| Ribosomal protein S5 | K02989 | K02988 |
| Ribosomal protein S7 | K02993 | K02992 |
| Ribosomal protein S8 | K02995 | K02994 |
| Ribosomal protein S9 | K02997 | K02996 |
| Seryl-tRNA synthetase | K01875 | K01875 |
| Arginyl-tRNA synthetase | K01887 | K01887 |
| DNA-directed RNA polymerase beta subunit | K03043 | K03043 |
| Ribosomal protein S13 | K02953 | K02952 |
4. How are SSU rRAN created?
The SSU rRAN sequences are created from the SILVA database (Release 132, Released: 13.12.2017). Sequences haven been truncated, which means unaligned nucleotides are removed.
5. How do I use PhySpeTree when I can't connect to the Internet?
When users can't connect to the Internet. They can download the HCP or SSU rRNA database to local and reconstruct species tree.
- SSU rRNA database: database16s.tar.gz
- HCP database: databasehcp.tar.gz
If you can not clink the hyperlink to obtain SSU rRNA and HCP databases, you can download from
ftp://23.105.208.65by FTP tools.
Use $ tar -zxvf database16s.tar.gz decompress the download database.
Use -db option setting the absolute path to decompression directory.