https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

You might learn a lot about that house—the rooms, the doors, the furniture—but you would miss the bigger story: the streets, the neighborhoods, and all the ways the city changes from one place to another.

Something similar happens when scientists study bacterial genomes one at a time.

Over the past decade, researchers have collected thousands of bacterial genomes. These genomes contain an enormous amount of information about how bacteria survive, adapt, and evolve. But comparing thousands of individual genomes can quickly become a computational maze.

That is where PANORAMA enters the story.

Developed by Jérôme Arnoux and colleagues, PANORAMA is a computational tool designed to explore bacterial pangenomes—the complete collection of genetic possibilities found across a species or group of related organisms. Instead of looking at every genome as an isolated object, the approach represents their shared and variable genetic features as a graph.

Think of this graph as a giant subway map.

Some stations appear on almost every route. These represent genes that are highly conserved. Other stations appear only on certain routes, representing genes that some bacteria possess while others do not. By looking at the entire network, scientists can begin to see not just *what genes exist*, but how they are organized and how biological systems are distributed across populations.

The researchers put PANORAMA to the test using 941 genomes of Pseudomonas aeruginosa, a bacterium important in human health. They used the tool to investigate biological systems, including bacterial defense mechanisms against viruses known as bacteriophages. They then expanded the analysis to more than 6,000 genomes from four Enterobacteriaceae species.

The result is more than a faster way to process data.

PANORAMA allows researchers to ask a bigger question: What can an entire microbial species do, genetically speaking?

By comparing pangenomes, the researchers could identify systems shared between species as well as distinctive features. They could also find recurring genomic locations where genetic material is inserted—clues that may reveal common evolutionary processes.

And this is perhaps the most exciting part of the story.

Every bacterial genome is like a page in a huge evolutionary book. Until recently, reading thousands of those pages together was difficult. PANORAMA provides a way to turn those pages into a map, allowing scientists to see patterns that might disappear when each genome is studied separately.

The study, published in PLOS Computational Biology in July 2026, presents PANORAMA as a foundation for large-scale comparative pangenomics. The software and accompanying analysis resources are openly available, giving other researchers the opportunity to explore microbial diversity themselves.

So the story is not really about one bacterium or one genome.

It is about changing the way we look at life.

Instead of asking, “What is inside this genome?”, scientists can increasingly ask, “What is the full genetic landscape of this species—and how did it become this way?”

And sometimes, when you stop looking at one house and finally see the whole city, the most interesting discoveries are hiding in the streets between them.

Read more at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013856

Address of the bookmark: https://github.com/pangenome/pggb

More at https://github.com/AntonBankevich/jumboDB

Address of the bookmark: https://github.com/AntonBankevich/jumboDB

Address of the bookmark: https://github.com/AdamCicherski/AlfaPang

Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

Address of the bookmark: https://github.com/skoren/PilonGrid

Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so aligning two 1-megabase bacterial genomes takes only 1.5 CPU-hours and 14 GB RAM. 

Address of the bookmark: https://github.com/ComparativeGenomicsToolkit/cactus

Part I – Basic Find Commands for Finding Files with Names
1. Find Files Using Name in Current Directory

Find all the files whose name is gene.txt in a current working directory.

# find . -name gene.txt

./gene.txt

2. Find Files Under Home Directory

Find all the files under /home directory with name gene.txt.

# find /home -name gene.txt

/home/gene.txt

3. Find Files Using Name and Ignoring Case

Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.

# find /home -iname gene.txt

./gene.txt
./Gene.txt

4. Find Directories Using Name

Find all directories whose name is Gene in / directory.

# find / -type d -name Gene

/Gene

5. Find fasta Files Using Name

Find all php files whose name is gene.fasta in a current working directory.

# find . -type f -name gene.fasta

./gene.fasta

6. Find all PHP Files in Directory

Find all fasta files in a directory.

# find . -type f -name "*.fasta"

./gene.fasta
./cancer.fasta
./allgene.fasta

Part II – Find Files Based on their Permissions
7. Find Files With 777 Permissions

Find all the files whose permissions are 777.

# find . -type f -perm 0777 -print

8. Find Files Without 777 Permissions

Find all the files without permission 777.

# find / -type f ! -perm 777

9. Find SGID Files with 644 Permissions

Find all the SGID bit files whose permissions set to 644.

# find / -perm 2644

10. Find Sticky Bit Files with 551 Permissions

Find all the Sticky Bit set files whose permission are 551.

# find / -perm 1551

11. Find SUID Files

Find all SUID set files.

# find / -perm /u=s

12. Find SGID Files

Find all SGID set files.

# find / -perm /g+s

13. Find Read Only Files

Find all Read Only files.

# find / -perm /u=r

14. Find Executable Files

Find all Executable files.

# find / -perm /a=x

15. Find Files with 777 Permissions and Chmod to 644

Find all 777 permission files and use chmod command to set permissions to 644.

# find / -type f -perm 0777 -print -exec chmod 644 {} \;

16. Find Directories with 777 Permissions and Chmod to 755

Find all 777 permission directories and use chmod command to set permissions to 755.

# find / -type d -perm 777 -print -exec chmod 755 {} \;

17. Find and remove single File

To find a single file called gene.txt and remove it.

# find . -type f -name "gene.txt" -exec rm -f {} \;

18. Find and remove Multiple File

To find and remove multiple files such as .fa or .gb, then use.

# find . -type f -name "*.fa" -exec rm -f {} \;

OR

# find . -type f -name "*.gb" -exec rm -f {} \;

19. Find all Empty Files

To file all empty files under certain path.

# find /tmp -type f -empty

20. Find all Empty Directories

To file all empty directories under certain path.

# find /tmp -type d -empty

21. File all Hidden Files

To find all hidden files, use below command.

# find /tmp -type f -name ".*"

Part III – Search Files Based On Owners and Groups
22. Find Single File Based on User

To find all or single file called gene.txt under / root directory of owner root.

# find / -user root -name gene.txt

23. Find all Files Based on User

To find all files that belongs to user Rahul under /home directory.

# find /home -user rahul

24. Find all Files Based on Group

To find all files that belongs to group Developer under /home directory.

# find /home -group developer

25. Find Particular Files of User

To find all .txt files of user Rahul under /home directory.

# find /home -user rahul -iname "*.txt"

Part IV – Find Files and Directories Based on Date and Time
26. Find Last 50 Days Modified Files

To find all the files which are modified 50 days back.

# find / -mtime 50

27. Find Last 50 Days Accessed Files

To find all the files which are accessed 50 days back.

# find / -atime 50

28. Find Last 50-100 Days Modified Files

To find all the files which are modified more than 50 days back and less than 100 days.

# find / -mtime +50 –mtime -100

29. Find Changed Files in Last 1 Hour

To find all the files which are changed in last 1 hour.

# find / -cmin -60

30. Find Modified Files in Last 1 Hour

To find all the files which are modified in last 1 hour.

# find / -mmin -60

31. Find Accessed Files in Last 1 Hour

To find all the files which are accessed in last 1 hour.

# find / -amin -60

Part V – Find Files and Directories Based on Size
32. Find 50MB Files

To find all 50MB files, use.

# find / -size 50M

33. Find Size between 50MB – 100MB

To find all the files which are greater than 50MB and less than 100MB.

# find / -size +50M -size -100M

34. Find and Delete 100MB Files

To find all 100MB files and delete them using one single command.

# find / -size +100M -exec rm -rf {} \;

35. Find Specific Files and Delete

Find all .gb files with more than 10MB and delete them using one single command.

# find / -type f -name *.gb -size +10M -exec rm {} \;

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

Address of the bookmark: https://github.com/vpc-ccg/lordfast