Mathias Currat, AGP Lab, Anthropology Unit - Department of Genetics and Evolution - University of Geneva
contact: mathias.currat@unige.ch
20.06.2017
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In order to simulate ancient Samples with SPLATCHE, please use the version Lin64_SerialSPLATCHEv1.0 (Linux version 64 bits)
provided here, following the instructions and using the example datasets given at http://www.splatche.com/.

The only modification to be done in order to use this version is to specify in the input file "GeneSamples.sam" the time at which each 
sample must be taken. It consists in adding a 6th (new) column with the generation number at which the sample has to be drawn.
Generation 0 means the beginning of the simulations and it can goes till the last simulated generation. In the example file with
1 layer (settings_test_1layer.txt), the duration of the simulation is 400 generations, so if one wants to sample at present
for this example, one has to add 400 at the end of the sample line in "GeneSamples.sam", as shown below. If one wants to sample
100 generations before the present (300 generations after the beginning of the simulation in that case), one has to add 300
at the end of the line, etc...

Note that if this last column is missing or the number given is larger than the number of simulated generations, then
the last generation is set by default (400 in the example below).

--------------------------
GeneSamples.sam
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6
ModSample1	30	0	20	20	400
ModSample2	30	0	20	0	400
ModSample3	30	0	0	20	400
AncSample4	30	0	-20	20	340
AncSample5	30	0	-30	25	300
AncSample6	30	0	5	40	295
#Name	#Size #Layer	#Lat #Long	#age
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Reference: 
Silva NM, Rio J & Currat M. Investigating population continuity with ancient DNA under a spatially explicit simulation framework. BMC Genetics (2017) 18:114