Hi Bilgenur,

It depends on what type of work you are going to perform. You can use MEGA4, for similar analysis part like MSA, ClustalW, Muscle, dendrogram prep etc. I will suggest you use the combination of software i.e. limited version of CLC and MEGA.

Hope that it will solve your purpose.

It depends on work to work basis but you can use

galaxy https://usegalaxy.org/

You could also try Unipro UGENE (http://ugene.unipro.ru), a free, open-source and cross-platform application.

Try iAssembler; Mira; CAP3;

Check the galaxy tool shed also for many tools related to sequence assembly

You could use R programm (cran.r-project.org). There are several packages on bioconductor (www.bioconductor.org) for the analysis of illumina chips

You don't say what it is you want to do. RNAseq? Assembly?

Nor what your personal computer is. Windows? Mac? Linux? If it's Windows you'll be limited to what you can do without installing another OS either dual-boot or in a Virtual Machine (e.g. VirtualBox).

There won't be anything that works like CLC, so be prepared to unlearn everything you know about CLC.

If you want a general purpose way of doing many things, then https://usegalaxy.org/ is a very good option as it only requires a web browser. If you want to become expert on a specific task or have complex requirements then the R/Bioconductor together with commandline skills route will be better.

Try InSilico DB (https://insilicodb.org) in combination with Gene-E, GenePattern, GenomeSpace.

It's free to access >200,000 manually curated public samples (microarray and RNASeq). There is also a service to store your private data and combine/compare it with public data.

Hope this helps.

Links:

InSilico DB: https://insilicodb.org

Gene-E: http://www.broadinstitute.org/cancer/software/GENE-E/

GenePattern: http://www.broadinstitute.org/cancer/software/genepattern/

GenomeSpace: https://gsui.genomespace.org/jsui/gsui.html

IGV: www.broadinstitute.org/igv/‎

GenomeSpace (www.genomespace.org) is a fantastic resource for integrating the use of multiple bioinformatics tools such as GALAXY, UCSC Genome Browser, Cytoscapte, GenePattern, Genomica, Integrative Genomics Vieweer [IGV], etc). It provides tools for formating the data as needed by each tool listed above. GenomeSpace provides the integrated workshop of more than 20 well-known bioinformatics tools.

http://www.genomespace.org

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