Metadata.

Metadata table for the LA and CU sequences used in this study (tab-separated format). It contains the following columns:

id—identifier of the sequence used in these analyses (corresponds to the tree tips);

POL Accession Number—GenBank [40] accession number for the pol part of the sequence;

ENV Accession Number—GenBank accession number for the env part of the sequence;

source—source of the data: LA or CU;

province_of_diagnostics—province of diagnostics for CU sequences, abroad for LA;

country_code—ISO2 code for the country of sampling;

country—country of sampling;

intregion—generalized location of sampling, includes the following values: Australia, Cuba, Eastern Africa, Eastern Asia, Middle Africa, Northern America, Northern Europe, Russia, South America, Southern Africa, Southern Asia, Southern Europe, Western Africa, Western Asia, Western Europe;

subregion—generalized location of sampling, includes the following values: Asia, Australia and New Zealand, Cuba, Europe, Northern America, Russia, South America, Sub-Saharan Africa;

region—generalized location of sampling, includes the following values: Africa, Americas, Asia, Cuba, Europe, Oceania;

sample_date—date of sampling;

diagnostics_date—date of diagnostics;

gender—gender of the infected individual: F or M;

risk_group—declared risk group: Bisexual, HT (heterosexual), or MSM (men-who-have-sex-with-men);

treated—treatment status: naive or treated;

subtype_annotated—pre-annotated HIV-1 subtype;

subtype_jpHMM—HIV-1 subtype detected by jpHMM;

subtype_consensus—HIV-1 subtype annotations used in this study: pre-annotated ones when compatible with jpHMM (e.g. matching jpHMM breakpoints for CRF19), otherwise jpHMM prediction;

subtype_tree—HIV-1 subtype detected by the phylogenetic trees in this study (same as consensus for the majority of the sequences, see Phylogenetic trees);

subtype_CRF_19_D—whether the sequence is compatible with CRF19 in its D part according to jpHMM: D if yes, empty otherwise;

subtype_CRF_19_G—whether the sequence is compatible with CRF19 in its G part according to jpHMM: G if yes, empty otherwise;

subtype_CRF_19_A1—whether the sequence is compatible with CRF19 in its A1 part according to jpHMM: A1 if yes, empty otherwise.

id—identifier of the sequence used in these analyses (corresponds to the tree tips);
POL Accession Number—GenBank [40] accession number for the pol part of the sequence;
ENV Accession Number—GenBank accession number for the env part of the sequence;
source—source of the data: LA or CU;
province_of_diagnostics—province of diagnostics for CU sequences, abroad for LA;
country_code—ISO2 code for the country of sampling;
country—country of sampling;
intregion—generalized location of sampling, includes the following values: Australia, Cuba, Eastern Africa, Eastern Asia, Middle Africa, Northern America, Northern Europe, Russia, South America, Southern Africa, Southern Asia, Southern Europe, Western Africa, Western Asia, Western Europe;
subregion—generalized location of sampling, includes the following values: Asia, Australia and New Zealand, Cuba, Europe, Northern America, Russia, South America, Sub-Saharan Africa;
region—generalized location of sampling, includes the following values: Africa, Americas, Asia, Cuba, Europe, Oceania;
sample_date—date of sampling;
diagnostics_date—date of diagnostics;
gender—gender of the infected individual: F or M;
risk_group—declared risk group: Bisexual, HT (heterosexual), or MSM (men-who-have-sex-with-men);
treated—treatment status: naive or treated;
subtype_annotated—pre-annotated HIV-1 subtype;
subtype_jpHMM—HIV-1 subtype detected by jpHMM;
subtype_consensus—HIV-1 subtype annotations used in this study: pre-annotated ones when compatible with jpHMM (e.g. matching jpHMM breakpoints for CRF19), otherwise jpHMM prediction;
subtype_tree—HIV-1 subtype detected by the phylogenetic trees in this study (same as consensus for the majority of the sequences, see Phylogenetic trees);
subtype_CRF_19_D—whether the sequence is compatible with CRF19 in its D part according to jpHMM: D if yes, empty otherwise;
subtype_CRF_19_G—whether the sequence is compatible with CRF19 in its G part according to jpHMM: G if yes, empty otherwise;
subtype_CRF_19_A1—whether the sequence is compatible with CRF19 in its A1 part according to jpHMM: A1 if yes, empty otherwise.
(TAB)