Review




Structured Review

Ridom GmbH bionumerics
Minimum spanning tree of certain spa types according to the county of origin of the samples. This was produced using the spa clustering in <t>BioNumerics</t> software (strains are identified according to spy type (different colours according to the legend) and county in Croatia (BB—Bjelovar-Bilogora county; BP—Brod-Posavina county; CZG—City of Zagreb county; I—Istra county; K—Karlovac County; KK—Koprivnica-Križevci county; KZ—Krapina-Zagorje county; LS—Lika-Senj county; M—Međimurje county; OB—Osijek-Baranja county; PS—Požega-Slavonia county; V—Varaždin county; ZG—Zagreb county; UN—unknown). Branch styles correspond to the relationship between strains (thick solid line for differences up to 2.2; thinner solid line for variations up to 3.4; the thinnest solid line for variations up to 4.59; dashed line for differences up to 5.8; and dotted line for variations above 5.8).
Bionumerics, supplied by Ridom GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics/pmc08066051-130-3-0
Average 90 stars, based on 1 article reviews
bionumerics - by Bioz Stars, 2026-09
90/100 stars

Images

1) Product Images from "Multi Locus Sequence Typing and spa Typing of Staphylococcus aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia"

Article Title: Multi Locus Sequence Typing and spa Typing of Staphylococcus aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia

Journal: Microorganisms

doi: 10.3390/microorganisms9040725

Minimum spanning tree of certain spa types according to the county of origin of the samples. This was produced using the spa clustering in BioNumerics software (strains are identified according to spy type (different colours according to the legend) and county in Croatia (BB—Bjelovar-Bilogora county; BP—Brod-Posavina county; CZG—City of Zagreb county; I—Istra county; K—Karlovac County; KK—Koprivnica-Križevci county; KZ—Krapina-Zagorje county; LS—Lika-Senj county; M—Međimurje county; OB—Osijek-Baranja county; PS—Požega-Slavonia county; V—Varaždin county; ZG—Zagreb county; UN—unknown). Branch styles correspond to the relationship between strains (thick solid line for differences up to 2.2; thinner solid line for variations up to 3.4; the thinnest solid line for variations up to 4.59; dashed line for differences up to 5.8; and dotted line for variations above 5.8).
Figure Legend Snippet: Minimum spanning tree of certain spa types according to the county of origin of the samples. This was produced using the spa clustering in BioNumerics software (strains are identified according to spy type (different colours according to the legend) and county in Croatia (BB—Bjelovar-Bilogora county; BP—Brod-Posavina county; CZG—City of Zagreb county; I—Istra county; K—Karlovac County; KK—Koprivnica-Križevci county; KZ—Krapina-Zagorje county; LS—Lika-Senj county; M—Međimurje county; OB—Osijek-Baranja county; PS—Požega-Slavonia county; V—Varaždin county; ZG—Zagreb county; UN—unknown). Branch styles correspond to the relationship between strains (thick solid line for differences up to 2.2; thinner solid line for variations up to 3.4; the thinnest solid line for variations up to 4.59; dashed line for differences up to 5.8; and dotted line for variations above 5.8).

Techniques Used: Produced, Software

Minimum spanning tree of certain sequence types (ST) according to the county of origin of the samples It was created using BioNumerics software. Colour coding corresponds to different counties in Croatia (BB—Bjelovar-Bilogora county; BP—Brod-Posavina county; CZG—City of Zagreb county; I—Istra county; K—Karlovac County; KK—Koprivnica-Križevci county; KZ—Krapina-Zagorje county; LS—Lika-Senj county; M—Međimurje county; OB—Osijek-Baranja county; PS—Požega-Slavonia county; SK—Šibenik-Knin county; SM—Sisak-Moslavina county; V—Varaždin county; Z—Zadar county; ZG—Zagreb county). Branch styles correspond to the relationship between strains (thick solid line for one locus variants; thinner solid line for double locus variants; the thinnest solid line for three locus variants; dashed line for four locus variants; and dotted line for five locus variants and above).
Figure Legend Snippet: Minimum spanning tree of certain sequence types (ST) according to the county of origin of the samples It was created using BioNumerics software. Colour coding corresponds to different counties in Croatia (BB—Bjelovar-Bilogora county; BP—Brod-Posavina county; CZG—City of Zagreb county; I—Istra county; K—Karlovac County; KK—Koprivnica-Križevci county; KZ—Krapina-Zagorje county; LS—Lika-Senj county; M—Međimurje county; OB—Osijek-Baranja county; PS—Požega-Slavonia county; SK—Šibenik-Knin county; SM—Sisak-Moslavina county; V—Varaždin county; Z—Zadar county; ZG—Zagreb county). Branch styles correspond to the relationship between strains (thick solid line for one locus variants; thinner solid line for double locus variants; the thinnest solid line for three locus variants; dashed line for four locus variants; and dotted line for five locus variants and above).

Techniques Used: Sequencing, Software

Related Articles

Software:

Article Title: Multi Locus Sequence Typing and spa Typing of Staphylococcus aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia
Article Snippet: Methods: Sequencing amplified gene sequences was conducted at Macrogen Europe. .. Ridom StaphType and BioNumerics software was used to analyze obtained sequences of spa and seven housekeeping genes. ..

Article Title: Make It Less difficile : Understanding Genetic Evolution and Global Spread of Clostridioides difficile
Article Snippet: .. Three publicly available schemes for C. difficile are available for cg- and/or wgMLST typing, and analysis can be performed using commercial software (e.g., BioNumerics, Ridom) or freely accessible online resources (e.g., EnteroBase). ..

Article Title: An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants
Article Snippet: .. However, larger-scale studies of the extent of genetic variation existing between persistent and transient strains are still needed. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG 1 caption a7 Haplo-ST, a tool for wgMLST profiling of Listeria monocytogenes from WGS reads. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Parameter Current wgMLST-based approaches for strain typing Haplo-ST BioNumerics Ridom SeqSphere+ Free availability No No Yes Database used for allelic nomenclature BIGSdb- Lm cgMLST.org BIGSdb- Lm Creates genome assemblies of isolates before allele calling Uses both assembly-based and assembly-free approaches Yes No (assembles genes instead of genomes) Expandable wgMLST schema No No Yes No. of loci used for wgMLST 4,804, fixed 1,701 (cgMLST) + 1,158 (accessory genome), fixed Currently 2,554, expandable Output wgMLST profiles, MST a wgMLST profiles, MST wgMLST profiles, allele sequences for wgMLST profiles, paralogous genes Cluster analysis features included with software Yes Yes No Types of cluster analysis possible MST MST, phylogenetic tree (software only provides concatenated allele sequences) Dendrograms and phylogenetic trees can be constructed with third-party software Can be used for strain typing of species other than L. monocytogenes Yes Yes Yes Automated curation tools (for assigning allele IDs) provided for new alleles Yes Yes No Open in a separate window a MST, minimum spanning tree. ..

Article Title: Make It Less difficile : Understanding Genetic Evolution and Global Spread of Clostridioides difficile .
Article Snippet: .. Three publicly available schemes for C. difficile are available for cgand/or wgMLST typing, and analysis can be performed using commercial software (e.g., BioNumerics, Ridom) or freely accessible online resources (e.g., EnteroBase). ..

Article Title: An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants
Article Snippet: .. 784 Current wgMLST-based approaches for strain typing Haplo-ST BioNumerics Ridom SeqSphere+ Free availability û û ü Database used for allelic nomenclature BIGSdb-Lm cgMLST.org BIGSdb-Lm Creates genomes assemblies of isolates before allele calling Uses both assemblybased and assembly- free approaches ü û (assembles genes instead of genomes) Expandable wgMLST schema û û ü Number of loci used for wgMLST 4804, fixed 1701 (cgMLST) + 1158 (accessory genome), fixed currently 2554, expandable Output wgMLST profiles, minimum spanning tree (MST) wgMLST profiles, MST wgMLST profiles, allele sequences for wgMLST profiles, paralogous genes Cluster analysis features included with software ü ü û Types of cluster analysis possible MST MST, phylogenetic tree (software only Dendrograms and phylogenetic trees can be constructed on D ecem ber 3, 2020 by guest http://aem .asm .org/ D ow nloaded from provides concatenated allele sequences) with third-party software Can be used for strain typing of species other than Listeria monocytogenes ü ü ü Automated curation tools (for assigning allele ID’s) provided for new alleles ü ü û 785 on D ecem ber 3, 2020 by guest http://aem .asm .org/ D ow nloaded from monocytogenes isolates. ..

Article Title: Outcome of EC/EFSA questionnaire (2016) on use of Whole Genome Sequencing (WGS) for food‐ and waterborne pathogens isolated from animals, food, feed and related environmental samples in EU/EFTA countries
Article Snippet: .. In house developed pipeline/ Commercially available software (e.g. BioNumerics , SeqSphere Ridom GmbH )/ Open source platform (e.g. Galaxy, Trimmomatic)/ Custom pipelines of different tools and software (e.g. CGE ). ..

Construct:

Article Title: An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants
Article Snippet: .. However, larger-scale studies of the extent of genetic variation existing between persistent and transient strains are still needed. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG 1 caption a7 Haplo-ST, a tool for wgMLST profiling of Listeria monocytogenes from WGS reads. table ft1 table-wrap mode="anchored" t5 TABLE 1 caption a7 Parameter Current wgMLST-based approaches for strain typing Haplo-ST BioNumerics Ridom SeqSphere+ Free availability No No Yes Database used for allelic nomenclature BIGSdb- Lm cgMLST.org BIGSdb- Lm Creates genome assemblies of isolates before allele calling Uses both assembly-based and assembly-free approaches Yes No (assembles genes instead of genomes) Expandable wgMLST schema No No Yes No. of loci used for wgMLST 4,804, fixed 1,701 (cgMLST) + 1,158 (accessory genome), fixed Currently 2,554, expandable Output wgMLST profiles, MST a wgMLST profiles, MST wgMLST profiles, allele sequences for wgMLST profiles, paralogous genes Cluster analysis features included with software Yes Yes No Types of cluster analysis possible MST MST, phylogenetic tree (software only provides concatenated allele sequences) Dendrograms and phylogenetic trees can be constructed with third-party software Can be used for strain typing of species other than L. monocytogenes Yes Yes Yes Automated curation tools (for assigning allele IDs) provided for new alleles Yes Yes No Open in a separate window a MST, minimum spanning tree. ..

Article Title: An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants
Article Snippet: .. 784 Current wgMLST-based approaches for strain typing Haplo-ST BioNumerics Ridom SeqSphere+ Free availability û û ü Database used for allelic nomenclature BIGSdb-Lm cgMLST.org BIGSdb-Lm Creates genomes assemblies of isolates before allele calling Uses both assemblybased and assembly- free approaches ü û (assembles genes instead of genomes) Expandable wgMLST schema û û ü Number of loci used for wgMLST 4804, fixed 1701 (cgMLST) + 1158 (accessory genome), fixed currently 2554, expandable Output wgMLST profiles, minimum spanning tree (MST) wgMLST profiles, MST wgMLST profiles, allele sequences for wgMLST profiles, paralogous genes Cluster analysis features included with software ü ü û Types of cluster analysis possible MST MST, phylogenetic tree (software only Dendrograms and phylogenetic trees can be constructed on D ecem ber 3, 2020 by guest http://aem .asm .org/ D ow nloaded from provides concatenated allele sequences) with third-party software Can be used for strain typing of species other than Listeria monocytogenes ü ü ü Automated curation tools (for assigning allele ID’s) provided for new alleles ü ü û 785 on D ecem ber 3, 2020 by guest http://aem .asm .org/ D ow nloaded from monocytogenes isolates. ..



Similar Products

90
Applied Maths bionumerics software program
Bionumerics Software Program, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/10__1016_slash_j__fm__2025__104762-66-6-11
Average 90 stars, based on 1 article reviews
bionumerics software program - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
Applied Maths bionumerics software program version 7.6
Bionumerics Software Program Version 7.6, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/pmc08202012-148-10-15
Average 90 stars, based on 1 article reviews
bionumerics software program version 7.6 - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
Applied Maths software program bionumerics
Software Program Bionumerics, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/10__4315_slash_0362___028x__jfp___18___338-72-14-16
Average 90 stars, based on 1 article reviews
software program bionumerics - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
Applied Maths software program bionumerics 7.5
Software Program Bionumerics 7.5, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/pmc07370939-132-7-10
Average 90 stars, based on 1 article reviews
software program bionumerics 7.5 - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
Applied Maths bionumerics 7.5 software program
Bionumerics 7.5 Software Program, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/pmc06051282-149-17-21
Average 90 stars, based on 1 article reviews
bionumerics 7.5 software program - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

90
Applied Maths bionumerics software program version 7.5
Bionumerics Software Program Version 7.5, supplied by Applied Maths, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bionumerics+software+program/bionumerics+software/pm28646667-85-13-18
Average 90 stars, based on 1 article reviews
bionumerics software program version 7.5 - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

Image Search Results