1. Felidae Phylogenetic Tree Mac Os 11
2. Felidae Phylogenetic Tree Mac Os Catalina

A free and open-source general purpose multiple sequence alignment program that enables you to perform profile alignments or phylogenetic trees

What's new in ClustalX 2.1:

Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores. Molecular Phylogenetics and Evolution 35(2):483-495. Index is applied to the Felidae species. After a comprehensive literature search, karyotype formulae, S/A I values and karyotype types of 23 species were determined. According to the S/A I values, a phylogenetic tree was drawn showing relationships among the species.

• Fixed bug 196 'clustalx: user feedback about use of secondary structure printed to console' - secondary structure is now used if specified in Alignment -> Alignment Parameters -> Secondary Structure Parameters UserParameters->getGui() should be used when ClustalW code needs to know if a function has been called from ClustalX
• Fixed bug 204 'Nexus alignment format contain invalid line' - the amino acid alphabet line has been removed
• Missing/corrupted file names in ClustalX status messages have been fixed
• Fixed bug 175 'msf/pileup files cannot be read if sequences names are all numbers' - this happened if a line such as 528244 .......... .......... .......... .......... .......... was present in the first block of the file

Read the full changelog

ClustalX is a streamlined OS X utility that provides the necessary tools to align DNA or protein sequences from within a user-friendly interface or a Terminal window.

ClustalX comes with support for numerous input formats, such as GDE, FASTA, NBRF/PIR, GCG9 RSF, Clustal, GCC/MSF and EMBL/Swiss-Prot.

In order to use ClustalX, you have to place each sequence in one file and arrange them one after another.

ClustalX's intuitive interface enables you to perform profile alignments, phylogenetic trees and multiple alignment in just a few easy steps.

From the Edit menu you can easily search for a String, remove gaps, clear sequences or range selections and switch between profiles.

By accessing the Alignment menu, you can easily align the sequences to the desired profile and open the Output Format Option window.

ClustalX also allows you to export to the NEXUS, Clustral, GDE, GCG/MSF and NBRF/PIR format.

In addition, ClustalX enables its users to choose between existing color sets or load a color parameter file with just a mouse click.

On top of that, users who are more comfortable performing all aforementioned tasks from a Terminal window, can download and use ClustalW.

Users that are interested in more advanced features like using secondary structures for profile alignment can use the 'Using ClustalX for multiple sequence' tutorial created by by Jarno Tuimala.

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ClustalX 2.1

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runs on:

Mac OS X (PPC & Intel)

file size:

12.6 MB

filename:

clustalx-2.1-macosx.dmg

main category:

Math/Scientific

developer:

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If you haven’t played it yet, the Felidae Phylogenetic Tree (aka, Felidae) is a 25-30min exploration of the feline evolutionary tree, with each species represented as a berry in said tree, containing images and factoids. I’m going to talk a bit about the process of making it, what worked and what didn’t (at least from my perspective), so I recommend you try it out first.

The Process

Felidae began as a note on a Game Ideas document I share with Dustin (the other half of Tea-Powered Games). It’s a casual document – the note starts with ‘Cats, cats, cats!’ and ends with ‘learning about animals in a fun way’. I’ve always been fascinated by all sorts of living creatures, but especially felines, having spent a lot of my pet-free childhood reading about them in the library. I wanted to make a game that wasn’t necessarily for nine-year-old me, but that she would have loved to explore alongside those books. And so, when I had finished working on the Broad Strokes Cooking Game, this ‘cat game’ became my next side project.

In many ways, the bulk of the game concept was there from week 1 (note that week 1 was March last year – we’ll get back to that). I quickly came up with a literal tree representing an evolutionary tree, and berries became a cluster of information tidbits about a species. The art style formed quite quickly as well – from a spreadsheet of feline information, I took the tiger’s information (an easy feline, most of the big cats are) and made a berry. Then I made the tree and other bits and bobs and threw it into Unity for testing. We had been using Unity for Dialogue, so I had some idea of how to use it, but this was a good chance to play with it myself. I ended up putting something together that worked, and I felt like the game was getting there. Five more felines got made (big cats again), I threw in a song and some moving clouds, then got some friends to play it. Consensus: it looks nice, it’s pleasant, but... I mean, can you do anything other than just read?

The first berry (tiger, left) and the last one (domestic cat, right). There were a lot of cats in between!

My first answer was ‘I’ll think about it’. After two or three months, I had done six out of forty-ish felines but there was still so much to do! Between double-checking info, drawing the berries and putting them into Unity, it was probably taking about five hours per feline. And so I made more berries for a while, until I was ready to tackle that whole ‘doing something other than reading’ problem, and enlisted Dustin for help. We came up with the Butterfly Mode, where you’re a small butterfly flying around the tree (with the camera zoomed in), uncovering berries which gain colour once you’ve inspected them. The goal was to explore the tree until you find all the berries – some were visible from the get-go, others looked like little buds, and yet others weren’t visible, just conspicuous dead-ends. If you manage to find all the berries you get a wallpaper with all the feline portraits and the game logo. Isn’t that neat? And if you prefer to just read, there’s always Eagle-Eye Mode, where you see the whole tree and everything is unlocked.

Positive

Art - The art style for the feline portraits was a good learning experience. I wanted to try something a bit different to improve my skills, and I liked how it ended up. Portraits aside, the game as a whole was more minimalist, consisting mostly of black silhouettes on coloured backgrounds, and I think it turned out to be quite pleasant. The portraits also made me more confident going into Elemental Flow’s art – as long as I had some kind of reference, I could probably do something nice on the art side.

Unity - I became more acquainted with Unity and its inspector tools, especially animations, text and laying out a scene. I’m placing art assets into Unity myself and laying out areas for Elemental Flow, so I’m glad I had time to play around in a project I made (I always worry about messing up someone else’s project and not knowing how to fix it).

Goal - I think the game is a nice experience, with information represented in an easy-to-understand manner, curated so people learn about all felines, even the less well-known ones. You also get a decent idea of how similar species are by looking at the tree (the usefulness of a phylogenetic tree in a nicer wrapper). The berries themselves give an information overview at a glance – you know a feline's geographic location, habitat, height and diet even if you don’t read any of the text.

Felidae Phylogenetic Tree Mac Os 11

A section of the wallpaper you can unlock. Cat portraits ahoy!

Negative

Release - Remember when I said Week 1 was in March ‘16? The berries and Eagle-Eye mode were mostly done by Nov ‘16, Butterfly Mode and the game as a whole around Feb ‘17. So the game itself was done in about a year... Then I hesitated. By that point Dialogue was out on Itch, to little fanfare. I thought Felidae could be good publicity for Tea-Powered Games, if I did more than what I usually do for my side games (put them online and tweet about them once). And yet, I was never sure what to do with it. We were focusing on getting Dialogue ready for Greenlight, then getting it Greenlit, then updating it for Steam, all the while working on Elemental Flow. Eventually I realised I wasn’t even sure what I was waiting for, and that marketing even a small free game is exhausting, so I released it without doing much else. I think the next time I want to do more with a game’s release, I’ll plan to from the get-go, otherwise I won’t beat myself up about it.

Exploration? - Butterfly Mode was meant to be the ‘gamier’ side of Felidae. Using exploration as a motivation, you collect berries and when you have them all, you get an out-of-game reward (if you want a new desktop background). I’m just not sure it really piqued people’s desire to explore. Did it feel like the equivalent of pixel-hunting to find all felines? Did people get bored and switch to Eagle-Eye Mode? I’d love to have some feedback on this. I made Butterfly Mode to encourage exploring a space that wasn’t specifically challenging, which is the sort of thing that works for me, but may not for other people (I don’t think challenge is necessary for a good experience, but some people find challenge to be synonymous with playing games).

Art - While I like how the game ended up and the portraits taught me something, it took a long time to make them. When I adapted what I learned for Elemental Flow I used filters and effects to alter photos, which makes things much quicker. Besides, after the tenth feline or so, I was getting diminishing returns on the learning front. While I knew after one or two berries how long the rest would take, and I was happy to put that time in, I probably should have looked at that (large) amount of time more critically.

Coding in Unity - I got comfortable with Unity’s graphical interfaces, but coding is still a hurdle for me; writing lines of code seems to put me in a completely different mind set. I like to think of myself as a jack-of-all-trades when it comes to games, but writing lines of code might have been a step too far (for now). And so, Dustin helped me revamp Eagle-Eye Mode, make Butterfly Mode, and generally overhaul things like how the berries and their text were stored and set up. Part of why I always have a side project going is that I like making a game entirely on my own, overcoming hurdles like not knowing how to compose at all (thank you Freesound!) and trying to make games using different programs. However, as I try more ambitious projects, I won’t shy away from finding other people to work with me.

Conclusion

Felidae Phylogenetic Tree Mac Os Catalina

In the end, I’m happy with Felidae, even if it took longer than I planned for it to be released. My previous side project (the Broad Strokes Cooking Game) felt like a tech demo for a longer game I wanted to make, whereas this one is self-contained and definitely finished. I hope others enjoy it too; while my side projects are chosen partially for me to learn something, they’re also games I would like to play myself (I just never know how many other people like the same sorts of things! Except cats, I’m sure lots of people like cats.)