How to analyze Principal Coordinates Analysis (PCoA) | Population genetics

How to analyze Principal Coordinate Analysis (PCoA) and PCA in GeneAlEx in Excel?
How to analyze Principal Coordinates Analysis (PCoA)?
How to PCoA using GeneAlEx Software?
How to PCA using GeneAlEx Software?
The Principal Coordinate Analysis and Principal Coordinate Analysis able to distinguish population variation? It is generally plotted on the dissimilarity matrix. While PCA is based on Euclidian distance, PCoA can differentiate dissimilarity matrices calculated from quantitative semi-quantitative variables.
#GeneAlEx 6.5 Software, #Tutorial, # Principal Coordinate Analysis (PCoA)
Principal Component Analysis (PCA), #GeneAlEx, #Molecular data analysis
Data input file formats for GeneAlEx 6.5
Import data matrix in GeneAlEx 6.5 software
Markers data formats files
SSR and SNP marker data
Single and Bi-allele’s data
Diploid and Haploid data
This video is about how to calculate Principal Coordinate Analysis (PCoA), PCA, Spatial analysis, Mantel Analysis.
Download GeneAlEx. 6.56b2 Software:
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Molecular data file formats video:
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GeneAlEx 6.5 Software is a very important software for population genetic data analysis in an Excel environment. GenAlEx 6.5 was developed by Peakall and Smouse 2006, 2012 and it offers a wide range of population genetic analysis tools. Molecular and genetic markers data analysis within the Microsoft Excel environment. GeneAlEx can install in both Windows and Mac OS computers. It is a user-friendly interface, rich graphical outputs for data exploration and publication, tools. It is very useful for data manipulation and export options to many other software packages. GenAlEx offers an ideal launching pad for population genetic analysis by students, teachers, and researchers alike.
In GeneAlEx 6.5b2 software tutorials, I am going to show how to download, install GeneAlEx Software in Excel?, How to create data file formats ?. How to create molecular data input file formats in Excel? Data input file formats for GeneAlEx 6.5
Import data matrix in GeneAlEx 6.5 software, Import sequence data in GeneAlEx 6.5 Software. GeneAlEx 6.5 Software input file formats. Molecular markers data formats files
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[@mishahdezlozano5635]

What a great videos! About the Mantel test.. where did you get the information from Matrix X and Y, you already have them for the analysis..thanks!

[@kanjanatinnaboot9468]

how to perform X,Y matric for mantel test?

[@cyrineouerghi9697]

can you do a video step by step for binary matrix in GenAlex for PCoA

[@ananou712]

Thank you for the video sir. But I have noticed that all your video are on SSR markers. What about SNPs? May you kindly help with SNPs file format to be used in GenAlex? Thank you

[@sciexpos]

First you need to convert snp data into genealex format or genetic format by using PGDSpider software. Best luck
www.cmpg.unibe.ch/software/PGDSpider/

[@ayeellapradeepgoud3377]

Good work sir...
Dose factorial analysis belonging to PCA analysis

[@sciexpos]

Yes both are same objectives but little difference is PCA is a linear combination of variables; Factor Analysis is a measurement model of a latent variable.

[@poojasihag9849]

Please make a video for binary data

[@magedmostafa66]

Good work sir, i have 2 question , can i calculate p value for Fst index? can i convert data to other forms like arlequin using genalex, i know there icon for export to multiple formats but actually did not work?
Thanks

[@sciexpos]

Thanks,I will look into it

[@stephaniegreige601]

I am trying to get a PcoA analysis.
I installed GenAix,
When I open it and go to Distance based, distance, genetic, I get an error message something avout data format and parameter.
Is it possible to share an email address in order to send a screenshot of what I am getting?
Thank you in advance

[@sciexpos]

For trouble shooting you need to follow files step

[@sciexpos]

I hope you have followed file preparation steps. First you need to copy all data and paste as numeric in another excel sheet or file. I think it will solved your problem. Best luck

[@samrariaz3396]

can u please guide me that how can i find genetic diversity of RAPD data on genalex and what is the exact of input file for this procedure and also did u know anything about popgene

[@sciexpos]

For RAPD markers diversity analysis can be done by Popgene and NTsys software

[@samrariaz3396]

@@sciexpos can u guide me how to upload data file on popgene because I m working on it but still I didn't know the correct input dta file that how can we make input file is it humble request please help me because I have to submit my thesis but still I am helpless

[@samrariaz3396]

Correct input dta file for rapd data

[@joaoricardobarnabe4963]

how can i put the gpd cordenates input?

[@sciexpos]

For that you need to use R software will give you much more functionality, All the best

[@kajalgoud8841]

Hi JP Goud

[@sciexpos]

Hi Didi 🙏🏻

[@anilkhar]

Kindly do not use music in the background. It is annoying

[@sciexpos]

Noted

[@aditimishra2385]

Can I have you email id sir ?

[@sciexpos]

Any doubt, you can ask me.