Presentation

This is a suite of badly written but useful programs to compute population genetics statistics using sequences data in fasta or phylip format. These programs are written using the Bio ++ library (Guéguen et al. 2013).

This include:

• seq_stat_2pop to compute statistics on two populations

• seq_stat_2pop_2N to compute statistics using only two diploid individuals. It was used in Allio et al. 2021.

• seq_stat_coding to compute statistics on only population using a alignment of coding sequences.

Last update of seq_stat_2pop (Vesion 2.0; source : seq_stat_2pop_bppV3.cpp) is written in Bio++ V3.

Author: Benoit Nabholz

References:

• Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, et al. 2013. Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution. Mol. Biol. Evol. 30:1745–1750.
• Allio R, Tilak M-K, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. 2021. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. Elife 10:e63167.

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Installation

You can use the static executable compiled for linux x64 computer (see Release). You can also compile the program assuming that you have Bio ++ installed (here the Bio++ library V2 is locally installed in $HOME/local/bpp/dev/ directory):

g++ --static -std=c++14 -g  seq_stat_2pop_bppV3.cpp -o seq_stat_2pop \
 -Wall -lbpp-phyl3 -lbpp-popgen3 -lbpp-seq3 -lbpp-core3  \
 -I$HOME/local/include -L$HOME/local/lib

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seq_stat_2pop

Usage:

seq_stat_2pop -seq [listSeq] -f [phylip or fasta] -coding [coding or non-coding] \
 -tvts [tv/ts ratio for computing NSS] -pop1 [prefix_pop1] -pop2 [prefix_pop2] \
 -outgroup [prefix_out] -o [out file]

Options :

• seq : a text file with the list of the sequence to analysed.
• f : sequence format fasta ot phylip
• coding : coding if protein coding sequences (only Standard Genetic Code)
• tvts : the transition over transversion ratio used for the computation of the number of synonymous site
• pop1 : the sequence name of the population 1 must include this prefix in their names (e.g. "PopA_ind1", "PopA_ind2" etc...).
• pop2 : the sequence name of the population 2 must include this prefix in their names (e.g. "PopB_ind1", "PopB_ind2" etc...).
• outgroup : the sequence name of the outgroup must include this prefix in their names.
• o : the name of the out file in csv format.

Statistics :

• Size : Size of the alignment (bp)
• S_Pop : Number of polymorphic site
• Pi_Pop : Tajima's estimator of nucleotides diversity
• W_Pop : Watterson's estimator of nucleotides diversity
• D_Pop : Tajima's D
• Dxy or Pi between : Average number of pairwise differences between sequences from two populations, excluding all comparisons between sequences within populations (Nei 1987; Cruickshank & Hahn, 2014)
• FstHud : Fst computed as in Hudson et al. 1992 Genetics 132:153 eq. 3
• FstNei_w : Fst computed as 1 - mean_Pi_Intra_Pop / Pi_total with mean weigthed using sample size (Nei 1982) with w = 1.* n_x/(n_x + n_y) and meanPiIntra = w*p_x + (1-w)*p_y. With n_x and n_y is the sample size of the population x and y respectively.
• FstNei_uw : Fst computed as 1 - mean_Pi_Intra_Pop / Pi_total (Nei 1982)
• PiInter : Inter popultaion nucleotides diversity
• Ts_Pop : Number of transition
• gc : GC content
• sizeOut : Size of outgroup sequence excluding gap and unresolved site (bp)
• divOut : Mean divergence between outgroup sequence and population n°2

Statistics for coding sequences :

• PS_Pop : Nucleotide diversity of synonymous sites
• PN_Pop : Nucleotide diversity of non-synonymous sites
• gc3 : GC content at the third codon position
• NSS_Pop : Number of synonymous site
• div_Syn_Out : Mean synonymous divergence between outgroup sequence and population n°2
• div_NonSyn_Out : Mean non-synonymous divergence between outgroup sequence and population n°2

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Example file

Two fasta sequences are store in the directory data/. There are two populations (Tguttata and Pacuticauda) but no outgroup.

To use the program:

# No outgroup are availbale in this example.

# store the sequence name in a list
ls data/*fasta >list_file

# compute sequence statistics according that the sequence are non-coding DNA 
seq_stat_2pop -seq list_file -f fasta -coding non-coding -tvts 1.0 \
 -pop1 Tguttata -pop2 Pacuticauda -outgroup NA -o out_non_coding.csv

# compute sequence statistics according that the sequence are coding DNA 
seq_stat_2pop -seq list_file -f fasta -coding coding -tvts 2.0 \
 -pop1 Tguttata -pop2 Pacuticauda -outgroup NA -o out_coding.csv

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seq_stat_2pop_2N

Usage of :

seq_stat_2pop_2N -seq [listSeq] -f [phylip or fasta] -pop1 [prefix_pop1] -pop2 [prefix_pop2] -o [out file]

Options :

• seq : a text file with the list of the sequence to analysed.
• f : sequence format fasta ot phylip
• pop1 : the sequence name of the population 1 must include this prefix in their names (e.g. "PopA_ind1", "PopA_ind2" etc...).
• pop2 : the sequence name of the population 2 must include this prefix in their names (e.g. "PopB_ind1", "PopB_ind2" etc...).
• o : the name of the out file in csv format.

Statistics :

• Fixed : Substitution between individual 1 and 2
• PrivatePop1 & PrivatePop2 : Heterozygous position unique to individual 1 and 2 respectively.
• Shared : Heterozygous position shared between individual 1 and 2
• Pi1 & Pi2 : Heterozygosity of individual 1 and 2
• PiTot : Tajima's estimator of nucleotides diversity of individual 1 and 2 combined

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seq_stat_coding

Usage:

seq_stat_coding -seq [listSeq] -f [phylip or fasta] -tstv [ts/tv ratio for computing NSS] -code [univ or mtmam or mtinv or mtechi] -o [out file]

Options :

• seq : a text file with the list of the sequence to analysed.
• f : sequence format fasta ot phylip
• tvts : the transition over transversion ratio used for the computation of the number of synonymous site
• code : genetic code (univ = standard universal; mt for mitochondrial
• o : the name of the out file in csv format.