3. PAReTT input and output
EXTENDED README
The following options are available through the main menu:
MAIN MENU:
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Choose one of the following options?
*) Check data availability
a) Get Divergence Times (pair)
b) Get Divergence Times (batch)
c) Get Evolutionary Timeline
d) Build a Time Tree
e) Print citation
f) Validate datafile
g) Calculate diversification rate (_r_)
q) Quit
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input is given as lower case '*','a', 'b', 'c', 'd', 'e', 'f', 'g', or 'q' e.g.
Choice: a
Brings up the menu to first check the TimeTree.org website for availability of divergence time data of your study species.
AVAILABILITY MENU:
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Choose one of the following options?
i) Individual
l) List
m) Main menu
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input is given as lower case 'i', 'l', or 'm' (return to main menu)
i) Individual
- Takes an individual species as input to look up data availability e.g. Chrysococcyx caprius
e.g.
Name: Chrysococcyx caprius
- Prints availability on screen in real time e.g.
Chrysococcyx caprius Not Available
l) List
- Takes a list of species as input in from a .txt input file e.g. Species.txt
e.g.
Input file in .txt format: Species.txt
- Prints availability on screen as real time monitoring
e.g.
Setophaga ruticilla Available 2022-06-16 15:58:27.073499
Hirundo rustica Available 2022-06-16 15:58:55.921913
Setophaga striata Available 2022-06-16 15:59:27.906028
- Provides option to save results to a file in .csv format with two columns, indicating the 'Species' and 'TimeTree.Data' availability e.g. Availability.csv
File name (.csv): Available.csv
e.g.
| Species | TimeTree.Data |
|---|---|
| Setophaga ruticilla | Available |
| Hirundo rustica | Available |
| Setophaga striata | Available |
- Takes a pair of species as input to look up divergence times e.g. Taxon a: Passer montanus, Taxon b: Halcyon senegalensis
Taxon a: Passer montanus
Taxon b: Halcyon senegalensis
- Prints divergence time in Millions of Years Ago (MYA) of pair on screen in real time
Passer montanus Halcyon senegalensis 70 2022-06-16 16:05:52.046194
- Takes a list of species as input to look up divergence times from a .txt input file e.g. Species.txt
Input file in .txt format: Species.txt
- Prints divergence time of pair on screen in MYA as real time monitoring
e.g.
Setophaga ruticilla Setophaga ruticilla 0 2022-06-16 16:08:59.721035
Setophaga ruticilla Hirundo rustica 35 2022-06-16 16:09:29.895971
Setophaga ruticilla Setophaga striata 3.52 2022-06-16 16:10:04.145198
Setophaga ruticilla DONE!
- Provides option to save results to a file in .csv format e.g. Output.csv
File name (.csv): Output.csv
e.g.
| Taxa1 | Taxa2 | Div.Time |
|---|---|---|
| Setophaga ruticilla | Setophaga ruticilla | 0 |
| Setophaga ruticilla | Hirundo rustica | 35 |
| Setophaga ruticilla | Setophaga striata | 3.52 |
| Hirundo rustica | Setophaga ruticilla | 35 |
| Hirundo rustica | Hirundo rustica | 0 |
| Hirundo rustica | Setophaga striata | 35 |
| Setophaga striata | Setophaga ruticilla | 3.52 |
| Setophaga striata | Hirundo rustica | 35 |
| Setophaga striata | Setophaga striata | 0 |
Brings up the menu options to retrieve the evolutionary timeline:
TIMELINE MENU:
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Choose one of the following options?
i) Individual
l) List
m) Main menu
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input is given as lower case 'i', 'l', or 'm' (return to main menu)
i) Individual
-
Takes an individual species as input to look up evolutionary timeline e.g. Passer montanus
-
Downloads .jpg result as name_timeline.jpg
l) List
- Takes a list of species as input in from a .txt input file e.g. Species.txt
Input file in .txt format: Species.txt
- Downloads .jpg result for each of the species in the list, as for individuals
Brings up the time tree menu options
TIME TREE MENU:
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Choose one of the following options?
t) Taxon
s) Species list
m) Main menu
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input is given as lower case 't', 's', or 'm' (return to main menu)
t) Taxon
- Takes the name for a taxon to get a time tree of all available species within the taxon e.g. Saxicola
Name: Saxicola
- Downloads the resulting time tree in the Newick format as Name_species.nwk
s) Species list
- Takes a list of species as input in from a .txt input file to generate a time tree e.g. Species.txt
Input file in .txt format: Species.txt
-
Downloads the resulting time tree in the Newick format as Filename.nwk
-
Stores replaced or missing species to a .txt file e.g. Unresolved_names.txt
e.g.
Calandrella cheleensis (replaced with Alauda gulgula)
Muscicapa striata (replaced with Muscicapa ruficauda)
Sialia mexicana (no substitute found)
Passer italiae (no substitute found)
Sialia currucoides (no substitute found)
Saxicola rubicola (no substitute found)
Prints the citation for the TimeTree resource
S. Kumar, G. Stecher, M. Suleski, and S.B. Hedges, 2017. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution 34: 1812-1819, DOI: 10.1093/molbev/msx116
Brings up the datafile validation menu options
VALIDATE MENU:
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a) Check missing
b) Replace missing
c) View tree
m) Main menu
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input is given as lower case 'a', 'b', 'c', or 'm' (return to main menu)
a) Check missing
-
Used to check for missing values from running a long list of species (>10 Species)
-
Takes the output file (.csv) from the divergence time function and checks for any missing values
e.g.
Taxa1 Taxa2 Div.Time Setophaga ruticilla Setophaga ruticilla 0 Setophaga ruticilla Hirundo rustica NA Setophaga ruticilla Setophaga striata 3.52 Hirundo rustica Setophaga ruticilla 35 Hirundo rustica Hirundo rustica 0 Hirundo rustica Setophaga striata NA Setophaga striata Setophaga ruticilla 3.52 Setophaga striata Hirundo rustica 35 Setophaga striata Setophaga striata 0 -
If no missing values are detected, will print 'No missing values'
-
If missing values are detected they are printed to the screen and an attempt will be made to look up those values
-
Asks for file name to store the missing values as a .csv file e.g. missing.csv
e.g.
Taxa1 Taxa2 Div.Time Setophaga ruticilla Hirundo rustica 35 Hirundo rustica Setophaga striata 35
b) Replace missing
-
Used to replace the missing values (divergence times) from a long list of species
-
Takes two input files, one with the divergence times and one with the missing values detected using 'Check missing'
-
Asks for file name to store the validated dataset of divergence times
e.g.
Taxa1 Taxa2 Div.Time Setophaga ruticilla Setophaga ruticilla 0 Setophaga ruticilla Hirundo rustica 35 Setophaga ruticilla Setophaga striata 3.52 Hirundo rustica Setophaga ruticilla 35 Hirundo rustica Hirundo rustica 0 Hirundo rustica Setophaga striata 35 Setophaga striata Setophaga ruticilla 3.52 Setophaga striata Hirundo rustica 35 Setophaga striata Setophaga striata 0
c) View tree
- Takes a newick tree as input and renders a basic display of tree topology
e.g.
Input tree file in .nwk format: Species.nwk
___ Setophaga_striata
_____________________________________________________|
_| |___ Setophaga_ruticilla
|
|_________________________________________________________ Hirundo_rustica
or
Input tree file in .nwk format: Saxicola_species.nwk
_______________________________ Saxicola_ferreus
________________________|
| |_______________________________ Saxicola_jerdoni
|
| _____________________________________________ Saxicola_insignis
| _|
_| | |_____________________________________________ Saxicola_caprata
| |
| | ___________ Saxicola_torquatus
| | _____________|
| | _______| |___________ Saxicola_dacotiae
| | | |
|________|_____________| |_________________________ Saxicola_tectes
| |
| |_________________________________ Saxicola_leucurus
|
| ________________________________ Saxicola_maurus
|_____________|
|________________________________ Saxicola_rubetra
- Calculates the diversification rate using the Magallon-Sanderson equation (Magallón and Sanderson, 2001)
When epsilon is 0:
When epsilon is >0:
- Takes three variables as input:
~ Species number (n), e.g.:
Species number (n): 12
~ Epsilon or Extinction rate fraction, e.g.:
Epsilon: 0.10
~ Divergence time (t) as crown/node age in Million Years Ago, e.g.:
Divergence time: 9
- Prints diversification rate on screen, e.g.:
Diversification rate (r): 0.198...
Exits program