cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.72564s
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ricinulei",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255798-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112049079
title: Cuneiform Tablet 1913.14.1506, Spurlock 1913.14.1506

description: [Text Description:] Account concerning silver, barley, and refined bitumen ❧ [Text or Publication Number Note:] Spurlock 1913.14.1506; CDLI P421358 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish White (10YR 9/2) Light Brown (5YR 6.5/4) Dark Gray (N 3/ 6.6% R) ❧ [Physical Object Note:] 10.1 x 6.9 x 2.9 cm (213g)
DOI: 10.15468/dl.fqur4p
title: Occurrence Download

description: A dataset containing 2730 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Euschistus servus (Say, 1832)"
 ]
}

 The dataset includes 2730 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011084-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112049049
title: Cuneiform Tablet 1913.14.1506, Spurlock 1913.14.1506

description: [Text Description:] Account concerning silver, barley, and refined bitumen ❧ [Text or Publication Number Note:] Spurlock 1913.14.1506; CDLI P421358 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish White (10YR 9/2) Light Brown (5YR 6.5/4) Dark Gray (N 3/ 6.6% R) ❧ [Physical Object Note:] 10.1 x 6.9 x 2.9 cm (213g)
DOI: 10.15468/dl.q268r8
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nilaparvata lugens (Stål, 1854)",
 "HasCoordinate is true",
 "Country is Japan",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0192580-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v56s7g
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parapalicus trituberculatus (Chen, 1981)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-14 42, 9 38, -7 26, -14 42))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012115-230828120925497/datasets/export for details.
DOI: 10.25549/inscriptifact-ouc112049080
title: Cuneiform Tablet 1913.14.1506, Spurlock 1913.14.1506

description: [Text Description:] Account concerning silver, barley, and refined bitumen ❧ [Text or Publication Number Note:] Spurlock 1913.14.1506; CDLI P421358 ❧ [Medium:] Clay ❧ [Script Note:] Non-Alphabetic Cuneiform ❧ [Physical Object Description:] Yellowish White (10YR 9/2) Light Brown (5YR 6.5/4) Dark Gray (N 3/ 6.6% R) ❧ [Physical Object Note:] 10.1 x 6.9 x 2.9 cm (213g)
DOI: 10.15468/dl.2agqhz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Glabropilumnus levimanus (Dana, 1852)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-14 42, 9 38, -7 26, -14 42))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012164-230828120925497/datasets/export for details.
DOI: 10.15468/dl.dve7na
title: Occurrence Download

description: A dataset containing 325992 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2022-11-02",
 "EventDate is less than or equal to 2022-12-02",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 325992 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0233168-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6pguj
title: Occurrence Download

description: A dataset containing 1049 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-103.42636 20.77566,-103.403 20.77566,-103.403 20.7925,-103.42636 20.7925,-103.42636 20.77566))"
 ]
}

 The dataset includes 1049 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036198-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z24w4v
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Benthopanope indica (De Man, 1887)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-14 42, 9 38, -7 26, -14 42))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012158-230828120925497/datasets/export for details.
DOI: 10.25549/inscriptifact-ouc112055860
title: P.Oxy.VI 890 Letter to a Strategus, P.Oxy.VI 890

description: [Text Description:] An incomplete letter from the executive of the local council at Oxyrhynchus to the state officer, giving a list of persons who owed money to the municipal treasury. ❧ [Text or Publication Number Note:] P.Oxy.VI 890, P.Oxy. 890, Spurlock 1914.21.0003 ❧ [Excavation Description:] Excavated by archaeologists, including Bernard Pyne Grenfell and Arthur Surridge Hunt, at an ancient rubbish dump near Oxyrhynchus in Egypt (28°32'N 30°40'E, modern el-Bahnasa). ❧ [Medium:] Papyrus ❧ [Script Note:] Greek ❧ [Physical Object Description:] Papyrus manuscript, 20.2 x 14.7 cm.
DOI: 10.15468/dl.8c5ntg
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerastium scaposum Boiss. & Heldr.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 39 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236893-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7dc6w
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eumedonus H.Milne Edwards, 1834",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-14 42, 9 38, -7 26, -14 42))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012160-230828120925497/datasets/export for details.
DOI: 10.25549/inscriptifact-ouc112055831
title: P.Oxy.VI 890 Letter to a Strategus, P.Oxy.VI 890

description: [Text Description:] An incomplete letter from the executive of the local council at Oxyrhynchus to the state officer, giving a list of persons who owed money to the municipal treasury. ❧ [Text or Publication Number Note:] P.Oxy.VI 890, P.Oxy. 890, Spurlock 1914.21.0003 ❧ [Excavation Description:] Excavated by archaeologists, including Bernard Pyne Grenfell and Arthur Surridge Hunt, at an ancient rubbish dump near Oxyrhynchus in Egypt (28°32'N 30°40'E, modern el-Bahnasa). ❧ [Medium:] Papyrus ❧ [Script Note:] Greek ❧ [Physical Object Description:] Papyrus manuscript, 20.2 x 14.7 cm.
DOI: 10.15468/dl.kzb99s
title: Occurrence Download

description: A dataset containing 339 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epinephelus cyanopodus (Richardson, 1846)"
 ]
}

 The dataset includes 339 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032428-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dkthzg
title: Occurrence Download

description: A dataset containing 15325 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((-8.13987 35.49989,29.8051 27.43695,43.43338 35.49989,43.43338 48.51166,-0.69631 44.06448,-8.13987 35.49989))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Posidonia oceanica (L.) Delile",
 "Year 2000-2023"
 ]
}

 The dataset includes 15325 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236905-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yweu6t
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Menticirrhus littoralis (Holbrook, 1847)"
 ]
}

 The dataset includes 99 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036187-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112055862
title: P.Oxy.VI 890 Letter to a Strategus, P.Oxy.VI 890

description: [Text Description:] An incomplete letter from the executive of the local council at Oxyrhynchus to the state officer, giving a list of persons who owed money to the municipal treasury. ❧ [Text or Publication Number Note:] P.Oxy.VI 890, P.Oxy. 890, Spurlock 1914.21.0003 ❧ [Excavation Description:] Excavated by archaeologists, including Bernard Pyne Grenfell and Arthur Surridge Hunt, at an ancient rubbish dump near Oxyrhynchus in Egypt (28°32'N 30°40'E, modern el-Bahnasa). ❧ [Medium:] Papyrus ❧ [Script Note:] Greek ❧ [Physical Object Description:] Papyrus manuscript, 20.2 x 14.7 cm.
DOI: 10.15468/dl.2895f7
title: Occurrence Download

description: A dataset containing 1161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guaiacum officinale L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1161 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003618-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dpugns
title: Occurrence Download

description: A dataset containing 192394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Occurrence evidence)",
 "GadmGid is one of (CAN, USA, NZL, AUS, BEL, FRA, ESP, PRT, AND, ITA, CHE, GBR.2_1, IRL, GBR, NLD, LUX, DEU)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ulex europaeus L."
 ]
}

 The dataset includes 192394 records from 727 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0258335-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112055863
title: P.Oxy.VI 890 Letter to a Strategus, P.Oxy.VI 890

description: [Text Description:] An incomplete letter from the executive of the local council at Oxyrhynchus to the state officer, giving a list of persons who owed money to the municipal treasury. ❧ [Text or Publication Number Note:] P.Oxy.VI 890, P.Oxy. 890, Spurlock 1914.21.0003 ❧ [Excavation Description:] Excavated by archaeologists, including Bernard Pyne Grenfell and Arthur Surridge Hunt, at an ancient rubbish dump near Oxyrhynchus in Egypt (28°32'N 30°40'E, modern el-Bahnasa). ❧ [Medium:] Papyrus ❧ [Script Note:] Greek ❧ [Physical Object Description:] Papyrus manuscript, 20.2 x 14.7 cm.
DOI: 10.15468/dl.j3u5tk
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fowleria punctulata (Rüppell, 1838)"
 ]
}

 The dataset includes 99 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036199-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxkzsd
title: Occurrence Download

description: A dataset containing 7689 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Avicennia marina (Forssk.) Vierh."
 ]
}

 The dataset includes 7689 records from 146 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0271262-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112055746
title: P.Oxy.VI 890 Letter to a Strategus, P.Oxy.VI 890

description: [Text Description:] An incomplete letter from the executive of the local council at Oxyrhynchus to the state officer, giving a list of persons who owed money to the municipal treasury. ❧ [Text or Publication Number Note:] P.Oxy.VI 890, P.Oxy. 890, Spurlock 1914.21.0003 ❧ [Excavation Description:] Excavated by archaeologists, including Bernard Pyne Grenfell and Arthur Surridge Hunt, at an ancient rubbish dump near Oxyrhynchus in Egypt (28°32'N 30°40'E, modern el-Bahnasa). ❧ [Medium:] Papyrus ❧ [Script Note:] Greek ❧ [Physical Object Description:] Papyrus manuscript, 20.2 x 14.7 cm.
DOI: 10.15468/dl.nfhb4v
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Spain",
 "Geometry POLYGON((-6.72922 35.95073,-4.45963 35.95073,-4.45963 37.06828,-6.72922 37.06828,-6.72922 35.95073))",
 "HasGeospatialIssue is false",
 "TaxonKey is Teline tribracteolata (Webb) Talavera & P.E.Gibbs"
 ]
}

 The dataset includes 32 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010047-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jpca8e
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Picea spinulosa (Griff.) Beissn."
 ]
}

 The dataset includes 103 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0379526-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjehfp
title: Occurrence Download

description: A dataset containing 937 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Thryssa hamiltonii Gray, 1835"
 ]
}

 The dataset includes 937 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032427-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/inscriptifact-ouc112054585
title: Baal Myth Sixth Tablet

description: [Text Description:] Shapsh helps Anat recover Baal's corpse, Anat destroys Mot, Baal is restored and fights Mot ❧ [Text or Publication Number Note:] KTU 1.6; CTA 6; CAT 1.6; KTU2 1.6; CTU 1.6; RS 2.[009]; RS 5.155 ❧ [Excavation Description:] Excavations at Ras Shamra 1930. Found in Library of the High Priest, p. t. 210-264, Acropolis, excavated by Claude F.-A. Schaeffer, Mission Archeologique Francaise. ❧ [Medium:] Clay ❧ [Script Note:] Alphabetic Cuneiform ❧ [Physical Object Description:] Clay tablet, 26.5 cm. X 19.5 cm., 2 fragments ❧ [Physical Object Note:] Grey clay, six columns, incomplete
DOI: 10.15468/dl.6jesr9
title: Occurrence Download

description: A dataset containing 980 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Marsilea strigosa Willd."
 ]
}

 The dataset includes 980 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003612-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d6r5kf
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Calcarius lapponicus)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000645-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xfdpb8
title: Occurrence Download

description: A dataset containing 3395 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Solidago gigantea",
 "Country is Austria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3395 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000646-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jq4zd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Calcarius lapponicus)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000647-250711103210423/datasets/export for details.
DOI: 10.5281/zenodo.15864696
title: Innate antiviral systems are major defensome components that influence prophage distribution in Acinetobacter baumannii

description: In this project, we have analysed the defensome of Acinetobacter baumannii with the aim of profiling different defense systems associated with particular prophage profiles, as well as to predict which systems are more effective and against which specific phages, associating both positively and negatively prophages to defense systems using machine learning techniques.

DOI (Biorxiv): https://doi.org/10.1101/2024.10.26.620419

Python scripts

Package versions: numpy 1.26.4 pandas 2.2.2

binary_matrix.py 

Generate a binary matrix of defense systems using genomes without prophages, as input of the Upset plot.

coocurr_matrix.py

Generate a matrix of defense systems coappearance, as input in the fig 2A.

defsys_pres_ann.py

Create a presence-absence matrix of defense systems.

freq_phages_bymlst.py

Get the most frequent prophages (10% of genomes) per MLST (provided in a list).

matrix_mlst_phages_freq.py

Generate two matrix of absolute and relative frequency, respectively, of prophages by frequent MLST group.

pres_aus_matrix_cl.py

Create a presence-absence matrix of prophages.

matrix_preaus_ml.py

Add to the presence-absence matrix of prophages two columns: one with the defense systems of each genome and another with the MLST group to which they belong.

cdhit_heamtap.py

Read CD-HIT output files and builds a variant matrix with the most prevalent clusters.

triangle_to_square.py

Read an upper triangular matrix (emboss format) format and converts it into a square matrix.

merge_dist.py

Merge both distance values (phylogenetic distance from the tree built in IQ-TREE and Kimura distance from the sequence alignment) from the same genome.and determine the MLST relationship between those genomes.

 

Phylogeny

Use assembly_seq.pl and uniq_sl.pl to build the initial multifasta with only the core genes, as input of MAFFT software. The generated MSA is processed using Clipkit, to eliminate gaps and keep the most informative regions. The processed MSA is used as input to iqTREE to generate the tree.

Circos

Circos were plotted using files generated by prepareForCircos2.pl. This script uses "defsys_presaus_ann.tsv", "logical_viruses.tsv" and a list of genomes of each MLST group to create the input file for the figure. These files are also provided.

README.txt

A more detailed version of the protocol used to generate the results and figures used in the paper.
DOI: 10.15468/dl.qs4sfr
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Qatar",
 "TaxonKey is Avicennia marina"
 ]
}

 The dataset includes 32 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000649-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.