Hengchi Chen
Bioinformatics & Evolutionary Genomics Group, VIB-UGent Center for Plant Systems Biology
The fossiler package can be readily installed via PYPI. An example command is given below.
virtualenv -p=python3 ENV (or python3/python -m venv ENV)
source ENV/bin/activate
pip install fossiler
Note that if users want to get the latest update, it's suggested to install from the source because the update on PYPI will be later than here of source. To install from source, the following command can be used.
git clone https://github.com/heche-psb/fossiler
cd fossiler
virtualenv -p=python3 ENV (or python3 -m venv ENV)
source ENV/bin/activate
pip install -r requirements.txt
pip install .
If there is permission problem in the installation, please try the following command.
pip install -e .
The implemented parameters are as below.
fossiler find
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-t, --tree, the tree topology file to assign fossil calibrations, default None
-mf, --mcmctreeformat, flag option, whether to get mcmctree format output
-wt, --wholetree, flag option, whether to use the whole angiosperm tree infomation instead of only user-defined local tree
-sc, --setconserved, flag option, whether to adopt the same maximum constraint as in Morris et al. (2018)
-gs, --getsp, flag option, whether to get species in the starting tree
-oo, --onlyone, flag option, whether to get only one species per order
-ut, --updatedtree, flag option, whether to use updated angiosperm phylogeny from our paper instead of APG IV
-cb, --combined, flag option, whether to use fossil calibrations based on combined database
-gt, --getaxonomy, get taxonomy information of a given species name, default None
-e, --email, email address to make requests to NCBI's Entrez utilities, default None
Below we give an example of using fossiler to obtain fossil calibrations.
fossiler find -mf -wt -sc -gs -ut -t inputfile
The inputfile is a tree file documenting the species names or taxonomy names. An example is as follows.
9 1
(((Alismatales,(Pandanales,Dioscoreales)),Acorales),(((Trochodendrales,Buxales),Proteales),(Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2)));
Species names should be joined by underlines. Note that it's allowed to append _ap1 and _ap2 at the end of a species name to create the starting tree file for WGD dating using wgd v2.
There will be 5 output files as below.
--inputfile.addtime
9 1
(((Alismatales,(Pandanales,Dioscoreales)'>0.5600<1.2863')'>0.8360<1.2863',Acorales)'>0.8360<1.2863',(((Trochodendrales,Buxales)'>1.1080<1.2863',Proteales)'>1.1080<1.2863',(Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2))'>1.1080<1.2863')'>1.2720<2.4720';
--inputfile.addtime_17sp
17 1
((((Potamogeton_acutifolius,(Spirodela_intermedia,Amorphophallus_konjac)),(Acanthochlamys_bracteata,(Dioscorea_alata,Dioscorea_rotundata))'>0.5600<1.2863')'>0.8360<1.2863',(Acorus_americanus,Acorus_tatarinowii))'>0.8360<1.2863',((((Tetracentron_sinense,Trochodendron_aralioides),(Buxus_austroyunnanensis,Buxus_sinica))'>1.1080<1.2863',(Nelumbo_nucifera,(Telopea_speciosissima,Protea_cynaroides)))'>1.1080<1.2863',(Aquilegia_coerulea_ap1,Aquilegia_coerulea_ap2))'>1.1080<1.2863')'>1.2720<2.4720';
--inputfile.addtime_sp17_species_list_lines
Potamogeton_acutifolius
Spirodela_intermedia
Amorphophallus_konjac
Acanthochlamys_bracteata
Dioscorea_alata
Dioscorea_rotundata
Acorus_americanus
Acorus_tatarinowii
Tetracentron_sinense
Trochodendron_aralioides
Buxus_austroyunnanensis
Buxus_sinica
Nelumbo_nucifera
Telopea_speciosissima
Protea_cynaroides
--inputfile.addtime_sp17_species_list_space
Potamogeton_acutifolius Spirodela_intermedia Amorphophallus_konjac Acanthochlamys_bracteata Dioscorea_alata Dioscorea_rotundata Acorus_americanus Acorus_tatarinowii Tetracentron_sinense Trochodendron_aralioides Buxus_austroyunnanensis Buxus_sinica Nelumbo_nucifera Telopea_speciosissima Protea_cynaroides Aquilegia_coerulea
--inputfile.addtime_taxonomy
9 1
(((Alismatales,(Pandanales,Dioscoreales)'>0.5600<1.2863')'>0.8360<1.2863',Acorales)'>0.8360<1.2863',(((Trochodendrales,Buxales)'>1.1080<1.2863',Proteales)'>1.1080<1.2863',(Ranunculales,Ranunculales))'>1.1080<1.2863')'>1.2720<2.4720';
The output file with suffix of 'addtime' is the tree file with fossil calibrations assigned on internal nodes. The output file with suffix of 'addtime_17sp' is the tree file with taxonomy represented in species and fossil calibrations assigned on internal nodes. The output file with suffix of 'addtime_sp17_species_list_lines' is the file documenting the species information line by line. The output file with suffix of 'addtime_sp17_species_list_space' is the file documenting the species information in one line separated by space. The output file with suffix of 'addtime_taxonomy' is the tree file with taxonomy represented in order and fossil calibrations assigned on internal nodes.