Commit 884dae3a0866bad5fea3db1e073c606af127d454 - aevol

+9

-1

debian/aevol.manpages less more

0	0	debian/aevol_create.1
1	1	debian/aevol_run.1
2		debian/aevol_run_X11.1
3	2	debian/aevol_modify.1
4	3	debian/aevol_propagate.1
	4	debian/aevol_misc_ancstats.1
	5	debian/aevol_misc_compute_pop_stats.1
	6	debian/aevol_misc_create_eps.1
	7	debian/aevol_misc_extract.1
	8	debian/aevol_misc_fixed_mutations.1
	9	debian/aevol_misc_gene_families.1
	10	debian/aevol_misc_lineage.1
	11	debian/aevol_misc_robustness.1
	12	debian/aevol_misc_view_generation.1

+23

-7

debian/aevol_create.1 less more

0		.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
1	2	.SH NAME
2	3	aevol \- an in silico experimental evolution platform
3	4	.SH SYNOPSIS

9	10	or
10	11	.B \-\-version
11	12	.br
12		.B aevol_create [\-f
13		.I param_file]
	13	.B aevol_create \fR[\fB\-v\fR] \fR[\fB\-f\fI PARAM_FILE\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-c\fI CFILE\fR] \fR[\fB\-p\fI PFILE\fR]
14	14	.SH DESCRIPTION
15	15	.B Aevol
16	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
17	17	.TP
18	18	.B aevol_create
19		create an experiment with setup as specified in
	19	create an experiment with setup as specified in
20	20	.I param_file
21	21	.SH OPTIONS
22	22	.TP
23	23	.B \-h, \-\-help
24		print this help, then exit
	24	print help, then exit
25	25	.TP
26	26	.B \-V, \-\-version
27	27	print version number, then exit
28		.TP
	28	.HP
29	29	.B \-f, \-\-file
30		.I param_file
	30	.I PARAM_FILE
	31	.br
31	32	specify parameter file (default: param.in)
	33	.HP
	34	.B \-o, \-\-out
	35	.I OUTDIR
	36	.br
	37	specify output directory (default "./")
	38	.HP
	39	.B \-c, \-\-chromosome
	40	.I CFILE
	41	.br
	42	load chromosome from given text file instead of generating it
	43	.HP
	44	.B \-p, \-\-plasmid
	45	.I PFILE
	46	.br
	47	load plasmid from given text file instead of generating it (params must allow plasmids)
32	48	.SH "SEE ALSO"
33	49	.B aevol_run, aevol_modify, aevol_propagate

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debian/aevol_misc_ancstats.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_ancstats \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_ancstats \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_ancstats \fB\-f\fI LINEAGE_FILE
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_ancstats
	19	issues statistics for the line of descent of a given individual.
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-f, \-\-file
	29	.I LINEAGE_FILE
	30	.br
	31	specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
	32	.SH "SEE ALSO"
	33	.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_compute_pop_stats.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_compute_pop_stats \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_compute_pop_stats \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_compute_pop_stats \fR[\fB\-i\fI INDEX\fR \| \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_compute_pop_stats
	19	issues population and replication statistics for each available backup from GENER1 to GENER2. These statistics are written in files global_pop_stats.out and stats/pop_stats/*.
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-i, \-\-index
	29	.I INDEX
	30	.br
	31	specify the index (ID in current generation) of the individual whose replication statistics should be outputted
	32	.HP
	33	.B \-r, \-\-rank
	34	.I RANK
	35	.br
	36	specify the rank of the individual whose replication statistics should be outputted
	37	.HP
	38	.B \-b, \-\-begin
	39	.I GENER
	40	.br
	41	specify the first generation for which the statistics should be computed
	42	.HP
	43	.B \-e, \-\-end
	44	.I GENER
	45	.br
	46	specify the last generation for which the statistics should be computed
	47	.SH "SEE ALSO"
	48	.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_create_eps.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_create_eps \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_create_eps \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_create_eps \fR[\fB\-i\fI INDEX\fR \| \fB\-r\fI RANK\fR] \fB\-g\fI GENER
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_create_eps
	19	produces several eps files describing an individual of this population
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-i, \-\-index
	29	.I INDEX
	30	.br
	31	specify the index (ID in current generation) of the individual
	32	.HP
	33	.B \-r, \-\-rank
	34	.I RANK
	35	.br
	36	specify the rank of the individual
	37	.HP
	38	.B \-g, \-\-gener
	39	.I GENER
	40	.br
	41	specify the generation of the individual
	42	.SH "SEE ALSO"
	43	.B aevol_create, aevol_modify, aevol_propagate, aevol_run

+58

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debian/aevol_misc_extract.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_extract \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_extract \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_extract \fR[\fB\-r\fI GENER\fR \| \fB\-p\fI POP_FILE\fR] \fR[\fB\-t\fI PHEN_FILE\fR] \fR[\fB\-s\fI SEQ_FILE\fR] \fR[\fB\-g\fI NUM_GU\fR] \fR[\fB\-b\fR]
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_extract
	19	extracts the genotype and/or data about the phenotype of individuals in the provided population and write them into text files easy to parse with e.g. matlab.
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-r
	29	.I GENER
	30	.br
	31	read generation GENER from a full aevol backup
	32	.HP
	33	.B \-p
	34	.I POP_FILE
	35	.br
	36	read the population saved in population file POP_FILE
	37	.HP
	38	.B \-t
	39	.I PHEN_FILE
	40	.br
	41	extract and save some infos about the phenotypes of the individuals to file PHEN_FILE
	42	.HP
	43	.B \-s
	44	.I SEQ_FILE
	45	.br
	46	extract and save the sequences of the individuals to file SEQ_FILE
	47	.HP
	48	.B \-g
	49	.I num_gu
	50	.br
	51	only treat this genetic unit (by default: treat all genetic units)
	52	.HP
	53	.B \-b
	54	.br
	55	only treat the best individual
	56	.SH "SEE ALSO"
	57	.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_fixed_mutations.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_fixed_mutations \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_fixed_mutations \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_fixed_mutations \fB\-f\fI LINEAGE_FILE
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_fixed_mutations
	19	issues the detailed list of mutations that occurred in the lineage of a given individual
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-f, \-\-file
	29	.I LINEAGE_FILE
	30	.br
	31	specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
	32	.SH "SEE ALSO"
	33	.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_gene_families.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_gene_families \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_gene_families \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_gene_families \fB\-f\fI LINEAGE_FILE
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_gene_families
	19	issues the detailed history of each gene family on the lineage of a given individual
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-f, \-\-file
	29	.I LINEAGE_FILE
	30	.br
	31	specify which lineage file to use. Lineage files are created by the ae_misc_lineage tool
	32	.SH "SEE ALSO"
	33	.B ae_misc_lineage, aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_lineage.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_lineage \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_lineage \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_lineage \fR[\fB\-i\fI INDEX\fR \| \fB\-r\fI RANK\fR] \fR[\fB\-b\fI GENER1\fR] \fB\-e\fI GENER2
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_lineage
	19	allows for the reconstruction of the lineage of a given individual. Requires the tree to have been recorded during evolution.
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-i, \-\-index
	29	.I INDEX
	30	.br
	31	specify the index (ID in current generation) of the individual whose lineage is to be reconstructed
	32	.HP
	33	.B \-r, \-\-rank
	34	.I RANK
	35	.br
	36	specify the rank of the individual whose lineage is to be reconstructed
	37	.HP
	38	.B \-b, \-\-begin
	39	.I GENER
	40	.br
	41	specify the generation up to which the lineage is to be reconstructed
	42	.HP
	43	.B \-e, \-\-end
	44	.I GENER
	45	.br
	46	specify the generation of the individual whose lineage is to be reconstructed
	47	.SH "SEE ALSO"
	48	.B aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_misc_robustness.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_robustness \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_robustness \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_robustness \fR\fB\-g\fI GENER\fR [\fB\-n\fI NBCHILDREN] \fR[\fB\-i\fI INDEX\fR \| \fB\-r\fI RANK\fR]
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_robustness
	19	computes the replication statistics of all the individuals of a given generation, like the proportion of neutral, beneficial, deleterious offsprings. This is done by simulating NBCHILDREN replications for each individual (1000 replications by default), with its mutation, rearrangement and transfer rates. Depending on those rates and genome size, there can be several mutations per replication. Those global statistics are written in stat/robustness_GENER.out, with one line per individual in the specified generation. The program also outputs detailed statistics for one of the individuals (the best one by default). The detailed statistics for this individual are written in stats/replication_GENER.out, with one line per simulated child of this particular individual.
	20
	21	.SH OPTIONS
	22	.TP
	23	.B \-h, \-\-help
	24	print help, then exit
	25	.TP
	26	.B \-V, \-\-version
	27	print version number, then exit
	28	.HP
	29	.B \-g, \-\-gener
	30	.I GENER
	31	.br
	32	specify the generation number for which the robustness statistics are desired
	33	.HP
	34	.B \-n, \-\-nb\-children
	35	.I NBCHILDREN
	36	.br
	37	specify the number of reproductions to simulate for each individual
	38	.HP
	39	.B \-i, \-\-index
	40	.I INDEX
	41	.br
	42	specify the index (ID in current generation) of the individual for whom detailed reproduction statistics are desired
	43	.HP
	44	.B \-r, \-\-rank
	45	.I RANK
	46	.br
	47	specify the rank of the individual for whom detailed reproduction statistics are desired
	48
	49	.SH "SEE ALSO"
	50	.B aevol_create, aevol_modify, aevol_propagate, aevol_run, aevol_misc_view_generation, aevol_misc_create_eps

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debian/aevol_misc_view_generation.1 less more

	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
	2	.SH NAME
	3	aevol \- an in silico experimental evolution platform
	4	.SH SYNOPSIS
	5	.B aevol_misc_view_generation \-h
	6	\|
	7	.B \-\-help
	8	.br
	9	.B aevol_misc_view_generation \-V
	10	\|
	11	.B \-\-version
	12	.br
	13	.B aevol_misc_view_generation \fB\-g\fI GENER
	14	.SH DESCRIPTION
	15	.B Aevol
	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
	17	.TP
	18	.B aevol_misc_view_generation
	19	allows one to visualize a generation using the exact same graphical outputs used in aevol_run.
	20	.SH OPTIONS
	21	.TP
	22	.B \-h, \-\-help
	23	print help, then exit
	24	.TP
	25	.B \-V, \-\-version
	26	print version number, then exit
	27	.HP
	28	.B \-g, \-\-gener
	29	.I GENER
	30	.br
	31	specify generation to visualize (default 0)
	32	.SH "SEE ALSO"
	33	.B aevol_create, aevol_modify, aevol_propagate, aevol_run

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debian/aevol_modify.1 less more

0		.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
1	2	.SH NAME
2	3	aevol \- an in silico experimental evolution platform
3	4	.SH SYNOPSIS

9	10	or
10	11	.B \-\-version
11	12	.br
12		.B aevol_modify \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-f\fI param_file\fR]
	13	.B aevol_modify \-g\fI GENER \fR[\fB\-f\fI param_file\fR]
13	14	.SH DESCRIPTION
14	15	.B Aevol
15	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
16	17	.TP
17	18	.B aevol_modify
18		modify an experiment as specified in
	19	modify an experiment as specified in
19	20	.I param_file
20	21	.SH OPTIONS
21	22	.TP
22	23	.B \-h, \-\-help
23		print this help, then exit
	24	print help, then exit
24	25	.TP
25	26	.B \-V, \-\-version
26	27	print version number, then exit
27	28	.HP
28	29	.B \-g, \-\-gener
29		.I GENERATION
	30	.I GENER
30	31	.br
31	32	specify generation number
32	33	.HP

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debian/aevol_propagate.1 less more

0		.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
1	2	.SH NAME
2	3	aevol \- an in silico experimental evolution platform
3	4	.SH SYNOPSIS

9	10	or
10	11	.B \-\-version
11	12	.br
12		.B aevol_propagate \fR[\fB\-g\fI GENERATION\fR] \fR[\fB\-i\fI in_dir\fR] \fR[\fB\-o\fI out_dir\fR] \fR[\fB\-v\fR]
	13	.B aevol_propagate \fR[\fB\-v\fR] \fR[\fB\-g\fI GENER\fR] \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-S\fI GENERALSEED\fR]
	14	.br
	15	.B aevol_propagate \fR[\fB\-v\fR] \fR[\fB\-g\fI GENER\fR] \fR[\fB\-i\fI INDIR\fR] \fR[\fB\-o\fI OUTDIR\fR] \fR[\fB\-s\fI SELSEED\fR] \fR[\fB\-m\fI MUTSEED\fR] \fR[\fB\-t\fI STOCHSEED\fR] \fR[\fB\-e\fI ENVVARSEED\fR] \fR[\fB\-n\fI ENVNOISESEED\fR]
13	16	.SH DESCRIPTION
14	17	.B Aevol
15	18	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
16	19	.TP
17	20	.B aevol_propagate
18		create a fresh copy of the experiment
	21	creates a fresh copy of the experiment as it was at the given generation. The generation number of the copy will be reset to 0. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. You can use the option \-S to do so. In this case, the random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). Alternatively, to change the random drawings for specific random processes only, do not use \-S but the options \-m, \-s, \-t, \-e, \-n (see below).
19	22	.SH OPTIONS
20	23	.TP
21	24	.B \-h, \-\-help
22		print this help, then exit
	25	print help, then exit
23	26	.TP
24	27	.B \-V, \-\-version
25	28	print version number, then exit
	29	.TP
	30	.B \-v, \-\-verbose
	31	be verbose
26	32	.HP
27	33	.B \-g, \-\-gener
28		.I GENERATION
	34	.I GENER
29	35	.br
30	36	specify generation number
	37	(default: that contained in file last_gener.txt, if any)
31	38	.HP
32	39	.B \-i, \-\-in
33		.I in_dir
	40	.I INDIR
34	41	.br
35	42	specify input directory (default ".")
36	43	.HP
37	44	.B \-o, \-\-out
38		.I in_dir
	45	.I OUTDIR
39	46	.br
40	47	specify output directory (default "./output")
41		.TP
42		.B \-v, \-\-verbose
43		be verbose
	48	.HP
	49	.B \-S, \-\-general\-seed
	50	.I GENERALSEED
	51	.br
	52	specify an integer to be used as a seed for random numbers. If you use aevol_propagate repeatedly to initialize several simulations, you should specify a different seed for each simulation, otherwise all simulations will yield exactly the same results. If you specify this general seed, random drawings will be different for all random processes enabled in your simulations (mutations, stochastic gene expression, selection, migration, environmental variation, environmental noise). To change the random drawings for a specific random process only, do not use \-S but the options below.
	53	.HP
	54	.B \-s, \-\-sel\-seed
	55	.I SELSEED
	56	.br
	57	specify an integer as a seed for random numbers needed for selection and migration (if spatial structure is enabled).
	58	.HP
	59	.B \-m, \-\-mut\-seed
	60	.I MUTSEED
	61	.br
	62	specify an integer as a seed for random numbers needed for mutations.
	63	.HP
	64	.B \-t, \-\-stoch\-seed
	65	.I STOCHSEED
	66	.br
	67	specify an integer as a seed for random numbers needed for stochastic gene expression.
	68	.HP
	69	.B \-e, \-\-env\-var\-seed
	70	.I ENVVARSEED
	71	.br
	72	specify an integer as a seed for random numbers needed for environmental variation.
	73	.HP
	74	.B \-n, \-\-env\-noise\-seed
	75	.I ENVNOISESEED
	76	.br
	77	specify an integer as a seed for random numbers needed for environmental noise.
44	78	.SH "SEE ALSO"
45	79	.B aevol_create, aevol_run, aevol_modify

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0		.TH AEVOL "1" "January 2014" "aevol 4.3" "User Manual"
	0	/#test with man \-l <file>
	1	.TH AEVOL "1" "July 2014" "aevol 4.4" "User Manual"
1	2	.SH NAME
2	3	aevol \- an in silico experimental evolution platform
3	4	.SH SYNOPSIS
4		.B aevol_run_X11 \-h
	5	.B aevol_run \-h
5	6	\|
6	7	.B \-\-help
7	8	.br
8		.B aevol_run_X11 \-V
	9	.B aevol_run \-V
9	10	\|
10	11	.B \-\-version
11	12	.br
12		.B aevol_run_X11 \fR[\fB\-r\fI GENERATION\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
	13	.B aevol_run \fR[\fB\-r\fI GENER\fR] \fR[\fB\-n\fI NB_GENER\fR] \fR[\fB\-tvwx\fR]
13	14	.SH DESCRIPTION
14	15	.B Aevol
15	16	is a simulation platform that allows one to let populations of digital organisms evolve in different conditions and study experimentally the mechanisms responsible for the structuration of the genome and the transcriptome.
16	17	.TP
17		.B aevol_run, aevol_run_X11
	18	.B aevol_run
18	19	run an aevol simulation.
19	20	.SH OPTIONS
20	21	.TP
21	22	.B \-h, \-\-help
22		print this help, then exit
	23	print help, then exit
23	24	.TP
24	25	.B \-V, \-\-version
25	26	print version number, then exit
26	27	.HP
	28	.B \-r, \-\-resume
	29	.I GENER
	30	.br
	31	specify generation to resume simulation at (default 0)
	32	.HP
27	33	.B \-n, \-\-nbgener
28	34	.I NB_GENER
29	35	.br
30		number of generations to be run
31		.HP
32		.B \-r, \-\-resume
33		.I GENERATION
34		.br
35		resume simulation at given generation
	36	specify number of generations to be run (default 1000)
36	37	.TP
37	38	.B \-t, \-\-text
38	39	use text files instead of binary files when possible

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aevol_run.1⏎